anno_start	anno_end	anno_text	entity_type	sentence	section
75	92	Thg1-like protein	protein_type	Template-dependent nucleotide addition in the reverse (3′-5′) direction by Thg1-like protein	TITLE
0	10	Structures	evidence	Structures of Thg1-like proteins provide insight into the template-dependent nucleotide addition in the reverse (3′-5′) direction.	ABSTRACT
14	32	Thg1-like proteins	protein_type	Structures of Thg1-like proteins provide insight into the template-dependent nucleotide addition in the reverse (3′-5′) direction.	ABSTRACT
0	17	Thg1-like protein	protein_type	Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner.	ABSTRACT
19	22	TLP	protein_type	Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner.	ABSTRACT
90	102	transfer RNA	chemical	Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner.	ABSTRACT
104	108	tRNA	chemical	Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner.	ABSTRACT
68	93	adenosine 5′-triphosphate	chemical	The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition.	ABSTRACT
95	98	ATP	chemical	The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition.	ABSTRACT
100	125	guanosine 5′-triphosphate	chemical	The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition.	ABSTRACT
127	130	GTP	chemical	The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition.	ABSTRACT
0	19	Structural analyses	experimental_method	Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3′-5′ direction.	ABSTRACT
27	30	TLP	protein_type	Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3′-5′ direction.	ABSTRACT
23	46	substrate binding sites	site	The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion.	ABSTRACT
111	126	reaction center	site	The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion.	ABSTRACT
145	149	Mg2+	chemical	The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion.	ABSTRACT
203	218	reaction center	site	The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion.	ABSTRACT
18	28	nucleotide	chemical	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
32	40	bound to	protein_state	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
45	64	second binding site	site	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
70	97	Watson-Crick hydrogen bonds	bond_interaction	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
144	159	5′-triphosphate	chemical	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
167	171	tRNA	chemical	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
189	204	reaction center	site	When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred.	ABSTRACT
9	32	3′-5′ elongation enzyme	protein_type	That the 3′-5′ elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution.	ABSTRACT
82	98	catalytic center	site	That the 3′-5′ elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution.	ABSTRACT
9	12	TLP	protein_type	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
17	21	Thg1	protein	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
35	45	tetrameric	oligomeric_state	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
64	68	tRNA	chemical	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
85	88	TLP	protein_type	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
115	119	Thg1	protein	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
123	159	tRNAHis-specific G−1 addition enzyme	protein_type	Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme.	ABSTRACT
5	12	tRNAHis	chemical	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
40	44	Thg1	protein	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
45	53	tetramer	oligomeric_state	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
54	62	subunits	structure_element	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
75	78	TLP	protein_type	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
80	84	tRNA	chemical	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
101	116	dimer interface	site	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
176	189	accepter stem	structure_element	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
209	217	flexible	protein_state	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
218	227	β-hairpin	structure_element	Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin.	ABSTRACT
13	32	mutational analyses	experimental_method	Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.	ABSTRACT
43	50	tRNAHis	chemical	Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.	ABSTRACT
54	62	bound to	protein_state	Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.	ABSTRACT
63	66	TLP	protein_type	Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.	ABSTRACT
90	94	Thg1	protein	Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.	ABSTRACT
117	120	TLP	protein_type	Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.	ABSTRACT
60	63	DNA	chemical	All polynucleotide chain elongation reactions, whether with DNA or RNA, proceed in the 5′-3′ direction.	INTRO
67	70	RNA	chemical	All polynucleotide chain elongation reactions, whether with DNA or RNA, proceed in the 5′-3′ direction.	INTRO
118	127	phosphate	chemical	This reaction involves the nucleophilic attack of a 3′-OH of the terminal nucleotide in the elongating chain on the α-phosphate of an incoming nucleotide.	INTRO
28	31	DNA	chemical	This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization).	INTRO
32	35	RNA	chemical	This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization).	INTRO
141	155	aminoacyl-tRNA	chemical	This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization).	INTRO
222	229	monomer	oligomeric_state	This elongation reaction of DNA/RNA chains is in clear contrast to the elongation of protein chains in which the high energy of the incoming aminoacyl-tRNA is not used for its own addition but for the addition of the next monomer (termed head polymerization).	INTRO
44	48	Thg1	protein	However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction.	INTRO
49	66	Thg1-like protein	protein_type	However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction.	INTRO
68	71	TLP	protein_type	However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction.	INTRO
100	104	tRNA	chemical	However, recent studies have shown that the Thg1/Thg1-like protein (TLP) family of proteins extends tRNA nucleotide chains in the reverse (3′-5′) direction.	INTRO
28	32	tRNA	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
58	83	adenosine 5′-triphosphate	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
85	88	ATP	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
90	115	guanosine 5′-triphosphate	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
117	120	GTP	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
194	220	nucleoside 5′-triphosphate	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
222	225	NTP	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
237	246	pppN-tRNA	chemical	In this case, the 5′-end of tRNA is first activated using adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleophilic attack of a 3′-OH on the incoming nucleotide [nucleoside 5′-triphosphate (NTP)] to yield pppN-tRNA.	INTRO
24	36	triphosphate	chemical	Thus, the energy in the triphosphate bond of the incoming nucleotide is not used for its own addition but is reserved for subsequent polymerization (that is, head polymerization) (Fig. 1).	INTRO
44	48	Thg1	protein	Top: Reaction scheme of 3′-5′ elongation by Thg1/TLP family proteins.	FIG
49	52	TLP	protein_type	Top: Reaction scheme of 3′-5′ elongation by Thg1/TLP family proteins.	FIG
47	66	DNA/RNA polymerases	protein_type	Bottom: Reaction scheme of 5′-3′ elongation by DNA/RNA polymerases.	FIG
23	27	Thg1	protein	In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction.	FIG
28	31	TLP	protein_type	In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction.	FIG
53	69	5′-monophosphate	chemical	In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction.	FIG
77	81	tRNA	chemical	In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction.	FIG
104	107	ATP	chemical	In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction.	FIG
108	111	GTP	chemical	In 3′-5′ elongation by Thg1/TLP family proteins, the 5′-monophosphate of the tRNA is first activated by ATP/GTP, followed by the actual elongation reaction.	FIG
23	42	DNA/RNA polymerases	protein_type	In 5′-3′ elongation by DNA/RNA polymerases, the energy of the incoming nucleotide is used for its own addition (tail polymerization).	FIG
60	70	eukaryotic	taxonomy_domain	The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis.	INTRO
71	75	Thg1	protein	The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis.	INTRO
77	104	tRNAHis guanylyltransferase	protein_type	The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis.	INTRO
190	197	tRNAHis	chemical	The best-characterized member of this family of proteins is eukaryotic Thg1 (tRNAHis guanylyltransferase), which catalyzes the nontemplated addition of a guanylate to the 5′-end of immature tRNAHis.	INTRO
5	14	guanosine	chemical	This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase.	INTRO
27	29	−1	residue_number	This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase.	INTRO
31	34	G−1	residue_name_number	This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase.	INTRO
39	46	tRNAHis	chemical	This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase.	INTRO
101	123	histidyl-tRNA synthase	protein_type	This guanosine at position −1 (G−1) of tRNAHis is a critical identity element for recognition by the histidyl-tRNA synthase.	INTRO
11	15	Thg1	protein	Therefore, Thg1 is essential to the fidelity of protein synthesis in eukaryotes.	INTRO
69	79	eukaryotes	taxonomy_domain	Therefore, Thg1 is essential to the fidelity of protein synthesis in eukaryotes.	INTRO
9	13	Thg1	protein	However, Thg1 homologs or TLPs are found in organisms in which G−1 is genetically encoded, and thus, posttranscriptional modification is not required.	INTRO
26	30	TLPs	protein_type	However, Thg1 homologs or TLPs are found in organisms in which G−1 is genetically encoded, and thus, posttranscriptional modification is not required.	INTRO
63	66	G−1	residue_name_number	However, Thg1 homologs or TLPs are found in organisms in which G−1 is genetically encoded, and thus, posttranscriptional modification is not required.	INTRO
27	31	TLPs	protein_type	This finding suggests that TLPs may have potential functions other than tRNAHis maturation.	INTRO
72	79	tRNAHis	chemical	This finding suggests that TLPs may have potential functions other than tRNAHis maturation.	INTRO
0	4	TLPs	protein_type	TLPs have been shown to catalyze 5′-end nucleotide addition to truncated tRNA species in vitro in a Watson-Crick template–dependent manner.	INTRO
73	77	tRNA	chemical	TLPs have been shown to catalyze 5′-end nucleotide addition to truncated tRNA species in vitro in a Watson-Crick template–dependent manner.	INTRO
17	21	TLPs	protein_type	This function of TLPs is not limited to tRNAHis but occurs efficiently with other tRNAs.	INTRO
40	47	tRNAHis	chemical	This function of TLPs is not limited to tRNAHis but occurs efficiently with other tRNAs.	INTRO
82	87	tRNAs	chemical	This function of TLPs is not limited to tRNAHis but occurs efficiently with other tRNAs.	INTRO
17	22	yeast	taxonomy_domain	Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage.	INTRO
32	37	Thg1p	protein	Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage.	INTRO
118	121	DNA	chemical	Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage.	INTRO
143	148	plant	taxonomy_domain	Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage.	INTRO
158	162	ICA1	protein	Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage.	INTRO
225	228	DNA	chemical	Furthermore, the yeast homolog (Thg1p) has been shown to interact with the replication origin recognition complex for DNA replication, and the plant homolog (ICA1) was identified as a protein affecting the capacity to repair DNA damage.	INTRO
32	36	TLPs	protein_type	These observations suggest that TLPs may have more general functions in DNA/RNA repair.	INTRO
72	75	DNA	chemical	These observations suggest that TLPs may have more general functions in DNA/RNA repair.	INTRO
76	79	RNA	chemical	These observations suggest that TLPs may have more general functions in DNA/RNA repair.	INTRO
41	45	Thg1	protein	The 3′-5′ addition reaction catalyzed by Thg1 occurs through three reaction steps.	INTRO
45	52	tRNAHis	chemical	In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate.	INTRO
74	88	ribonuclease P	protein_type	In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate.	INTRO
94	105	pre-tRNAHis	chemical	In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate.	INTRO
123	126	ATP	chemical	In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate.	INTRO
155	162	tRNAHis	chemical	In the first step, the 5′-monophosphorylated tRNAHis, which is cleaved by ribonuclease P from pre-tRNAHis, is activated by ATP, creating a 5′-adenylylated tRNAHis intermediate.	INTRO
46	49	GTP	chemical	In the second step, the 3′-OH of the incoming GTP attacks the activated intermediate, yielding pppG−1-tRNAHis.	INTRO
95	109	pppG−1-tRNAHis	chemical	In the second step, the 3′-OH of the incoming GTP attacks the activated intermediate, yielding pppG−1-tRNAHis.	INTRO
13	26	pyrophosphate	chemical	Finally, the pyrophosphate is removed, and mature pG−1-tRNAHis is created.	INTRO
50	62	pG−1-tRNAHis	chemical	Finally, the pyrophosphate is removed, and mature pG−1-tRNAHis is created.	INTRO
4	21	crystal structure	evidence	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
25	30	human	species	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
31	35	Thg1	protein	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
37	43	HsThg1	protein	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
60	74	catalytic core	site	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
117	145	5′-3′ nucleotide polymerases	protein_type	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
155	177	T7 DNA/RNA polymerases	protein_type	The crystal structure of human Thg1 (HsThg1) shows that its catalytic core shares structural homology with canonical 5′-3′ nucleotide polymerases, such as T7 DNA/RNA polymerases.	INTRO
27	51	3′-5′ elongation enzymes	protein_type	This finding suggests that 3′-5′ elongation enzymes are related to 5′-3′ polymerases and raises important questions on why 5′-3′ polymerases predominate in nature.	INTRO
67	84	5′-3′ polymerases	protein_type	This finding suggests that 3′-5′ elongation enzymes are related to 5′-3′ polymerases and raises important questions on why 5′-3′ polymerases predominate in nature.	INTRO
123	140	5′-3′ polymerases	protein_type	This finding suggests that 3′-5′ elongation enzymes are related to 5′-3′ polymerases and raises important questions on why 5′-3′ polymerases predominate in nature.	INTRO
4	21	crystal structure	evidence	The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1.	INTRO
25	28	TLP	protein_type	The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1.	INTRO
34	56	Bacillus thuringiensis	species	The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1.	INTRO
88	98	tetrameric	oligomeric_state	The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1.	INTRO
112	123	active-site	site	The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1.	INTRO
142	148	HsThg1	protein	The crystal structure of TLP from Bacillus thuringiensis shows that it shares a similar tetrameric assembly and active-site architecture with HsThg1.	INTRO
17	26	structure	evidence	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
30	46	Candida albicans	species	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
47	51	Thg1	protein	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
53	59	CaThg1	protein	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
61	75	complexed with	protein_state	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
76	83	tRNAHis	chemical	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
101	105	tRNA	chemical	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
129	144	reaction center	site	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
192	210	DNA/RNA polymerase	protein_type	Furthermore, the structure of Candida albicans Thg1 (CaThg1) complexed with tRNAHis reveals that the tRNA substrate accesses the reaction center from a direction opposite to that of canonical DNA/RNA polymerase.	INTRO
17	36	structural analysis	experimental_method	However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound.	INTRO
52	59	tRNAHis	chemical	However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound.	INTRO
104	107	GTP	chemical	However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound.	INTRO
113	122	not bound	protein_state	However, in this structural analysis, the 5′-end of tRNAHis was not activated and the second substrate (GTP) was not bound.	INTRO
22	28	solved	experimental_method	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
33	42	structure	evidence	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
46	49	TLP	protein_type	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
59	80	methanogenic archaeon	taxonomy_domain	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
81	107	Methanosarcina acetivorans	species	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
109	114	MaTLP	protein	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
116	131	in complex with	protein_state	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
132	144	ppptRNAPheΔ1	chemical	Here, we successfully solved the structure of TLP from the methanogenic archaeon Methanosarcina acetivorans (MaTLP) in complex with ppptRNAPheΔ1, which mimics the activated intermediate of the repair substrate.	INTRO
9	12	TLP	protein_type	Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP.	INTRO
17	21	Thg1	protein	Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP.	INTRO
35	45	tetrameric	oligomeric_state	Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP.	INTRO
72	76	tRNA	chemical	Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP.	INTRO
101	104	TLP	protein_type	Although TLP and Thg1 have similar tetrameric organization, the mode of tRNA binding is different in TLP.	INTRO
29	38	structure	evidence	Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA.	INTRO
52	55	GTP	chemical	Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA.	INTRO
64	69	GDPNP	chemical	Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA.	INTRO
112	134	Watson-Crick base pair	bond_interaction	Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA.	INTRO
140	143	C72	residue_name_number	Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA.	INTRO
172	176	tRNA	chemical	Furthermore, we obtained the structure in which the GTP analog (GDPNP) was inserted into this complex to form a Watson-Crick base pair with C72 at the 3′-end region of the tRNA.	INTRO
22	32	structures	evidence	On the basis of these structures, we discuss the reaction mechanism of template-dependent reverse (3′-5′) polymerization in comparison with canonical 5′-3′ polymerization.	INTRO
33	45	ppptRNAPheΔ1	chemical	Anticodon-independent binding of ppptRNAPheΔ1 to MaTLP	RESULTS
49	54	MaTLP	protein	Anticodon-independent binding of ppptRNAPheΔ1 to MaTLP	RESULTS
9	32	biochemical experiments	experimental_method	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
53	65	ppptRNAPheΔ1	chemical	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
90	97	tRNAPhe	chemical	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
124	126	G1	residue_name_number	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
131	138	deleted	experimental_method	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
217	221	Thg1	protein	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
222	225	TLP	protein_type	Previous biochemical experiments have suggested that ppptRNAPheΔ1, in which the 5′-end of tRNAPhe was triphosphorylated and G1 was deleted, can be an efficient substrate for the repair reaction (guanylyl transfer) of Thg1/TLP.	RESULTS
25	32	crystal	evidence	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
36	41	MaTLP	protein	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
42	56	complexed with	protein_state	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
57	69	ppptRNAPheΔ1	chemical	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
74	80	solved	experimental_method	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
85	94	structure	evidence	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
155	158	TLP	protein_type	Therefore, we prepared a crystal of MaTLP complexed with ppptRNAPheΔ1 and solved its structure to study the template-directed 3′-5′ elongation reaction by TLP (fig. S1).	RESULTS
4	11	crystal	evidence	The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit.	RESULTS
24	29	dimer	oligomeric_state	The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit.	RESULTS
33	36	TLP	protein_type	The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit.	RESULTS
38	39	A	structure_element	The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit.	RESULTS
44	45	B	structure_element	The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit.	RESULTS
65	69	tRNA	chemical	The crystal contained a dimer of TLP (A and B molecules) and one tRNA in an asymmetric unit.	RESULTS
4	10	dimers	oligomeric_state	Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2).	RESULTS
18	25	crystal	evidence	Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2).	RESULTS
49	54	dimer	oligomeric_state	Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2).	RESULTS
58	64	dimers	oligomeric_state	Two dimers in the crystal further assembled as a dimer of dimers by the crystallographic twofold axis (Fig. 2).	RESULTS
5	15	tetrameric	oligomeric_state	This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex.	RESULTS
16	25	structure	evidence	This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex.	RESULTS
55	63	TLP-tRNA	complex_assembly	This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex.	RESULTS
101	112	CaThg1-tRNA	complex_assembly	This tetrameric structure and 4:2 stoichiometry of the TLP-tRNA complex are the same as those of the CaThg1-tRNA complex.	RESULTS
21	23	AB	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
28	30	CD	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
31	37	dimers	oligomeric_state	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
41	51	tetrameric	oligomeric_state	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
52	58	CaThg1	protein	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
110	123	accepter stem	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
141	148	tRNAHis	chemical	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
154	156	AB	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
157	162	dimer	oligomeric_state	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
186	188	CD	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
189	194	dimer	oligomeric_state	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
199	209	tetrameric	oligomeric_state	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
210	215	MaTLP	protein	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
251	255	tRNA	chemical	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
283	287	tRNA	chemical	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
288	301	accepter stem	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
306	318	elbow region	structure_element	However, whereas the AB and CD dimers of tetrameric CaThg1 play different roles, respectively recognizing the accepter stem and anticodon of tRNAHis, the AB dimer and its symmetry mate (CD dimer) on tetrameric MaTLP independently bind one molecule of tRNA (fig. S2), recognizing the tRNA accepter stem and elbow region.	RESULTS
38	43	MaTLP	protein	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
50	85	anticodon-independent repair enzyme	protein_type	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
127	137	MaTLP-tRNA	complex_assembly	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
175	181	CaThg1	protein	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
193	196	G−1	residue_name_number	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
230	233	His	residue_name	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
293	297	tRNA	chemical	Thus, consistent with the notion that MaTLP is an anticodon-independent repair enzyme, the anticodon was not recognized in the MaTLP-tRNA complex, whereas the binding mode of CaThg1 is for the G−1 addition reaction, therefore the His anticodon has to be recognized (see “Dual binding mode for tRNA repair”).	RESULTS
0	9	Structure	evidence	Structure of the MaTLP complex with ppptRNAPheΔ1.	FIG
17	22	MaTLP	protein	Structure of the MaTLP complex with ppptRNAPheΔ1.	FIG
23	35	complex with	protein_state	Structure of the MaTLP complex with ppptRNAPheΔ1.	FIG
36	48	ppptRNAPheΔ1	chemical	Structure of the MaTLP complex with ppptRNAPheΔ1.	FIG
26	30	tRNA	chemical	Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer.	FIG
42	54	ppptRNAPheΔ1	chemical	Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer.	FIG
59	67	bound to	protein_state	Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer.	FIG
72	77	MaTLP	protein	Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer.	FIG
78	83	dimer	oligomeric_state	Left: One molecule of the tRNA substrate (ppptRNAPheΔ1) is bound to the MaTLP dimer.	FIG
4	6	AB	structure_element	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
11	13	CD	structure_element	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
14	20	dimers	oligomeric_state	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
33	42	dimerized	oligomeric_state	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
90	100	tetrameric	oligomeric_state	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
101	110	structure	evidence	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
112	117	dimer	oligomeric_state	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
121	127	dimers	oligomeric_state	The AB and CD dimers are further dimerized by the crystallographic twofold axis to form a tetrameric structure (dimer of dimers).	FIG
4	6	CD	structure_element	The CD dimer is omitted for clarity.	FIG
7	12	dimer	oligomeric_state	The CD dimer is omitted for clarity.	FIG
4	17	accepter stem	structure_element	The accepter stem of the tRNA is recognized by molecule A (yellow), and the elbow region by molecule B (blue).	FIG
25	29	tRNA	chemical	The accepter stem of the tRNA is recognized by molecule A (yellow), and the elbow region by molecule B (blue).	FIG
76	88	elbow region	structure_element	The accepter stem of the tRNA is recognized by molecule A (yellow), and the elbow region by molecule B (blue).	FIG
4	13	β-hairpin	structure_element	The β-hairpin region of molecule B is shown in red.	FIG
4	16	elbow region	structure_element	The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP.	RESULTS
24	28	tRNA	chemical	The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP.	RESULTS
61	70	β-hairpin	structure_element	The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP.	RESULTS
88	93	MaTLP	protein	The elbow region of the tRNA substrate was recognized by the β-hairpin of molecule B of MaTLP.	RESULTS
33	37	R215	residue_name_number	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
45	54	β-hairpin	structure_element	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
65	70	MaTLP	protein	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
76	91	hydrogen-bonded	bond_interaction	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
99	108	phosphate	chemical	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
119	122	U55	residue_name_number	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
127	130	G57	residue_name_number	The N atoms in the side chain of R215 in the β-hairpin region of MaTLP were hydrogen-bonded to the phosphate groups of U55 and G57.	RESULTS
18	22	S213	residue_name_number	The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2).	RESULTS
43	58	hydrogen-bonded	bond_interaction	The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2).	RESULTS
66	75	phosphate	chemical	The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2).	RESULTS
86	89	G57	residue_name_number	The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2).	RESULTS
97	101	tRNA	chemical	The O atom on the S213 side chain was also hydrogen-bonded to the phosphate moiety of G57 of the tRNA (Fig. 2).	RESULTS
5	14	β-hairpin	structure_element	This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex.	RESULTS
26	36	disordered	protein_state	This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex.	RESULTS
44	61	crystal structure	evidence	This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex.	RESULTS
69	80	CaThg1-tRNA	complex_assembly	This β-hairpin region was disordered in the crystal structure of the CaThg1-tRNA complex.	RESULTS
4	17	accepter stem	structure_element	The accepter stem of the tRNA substrate was recognized by molecule A of MaTLP.	RESULTS
25	29	tRNA	chemical	The accepter stem of the tRNA substrate was recognized by molecule A of MaTLP.	RESULTS
72	77	MaTLP	protein	The accepter stem of the tRNA substrate was recognized by molecule A of MaTLP.	RESULTS
15	17	G2	residue_name_number	The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2).	RESULTS
36	51	hydrogen-bonded	bond_interaction	The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2).	RESULTS
73	77	R136	residue_name_number	The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2).	RESULTS
104	113	phosphate	chemical	The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2).	RESULTS
132	136	N137	residue_name_number	The N7 atom of G2 at the 5′-end was hydrogen-bonded to the N atom of the R136 side chain, whereas the α-phosphate was bonded to the N137 side chain (Fig. 2).	RESULTS
0	4	R136	residue_name_number	R136 was also hydrogen-bonded to the base of C72 (the Watson-Crick bond partner of ΔG1).	RESULTS
14	29	hydrogen-bonded	bond_interaction	R136 was also hydrogen-bonded to the base of C72 (the Watson-Crick bond partner of ΔG1).	RESULTS
45	48	C72	residue_name_number	R136 was also hydrogen-bonded to the base of C72 (the Watson-Crick bond partner of ΔG1).	RESULTS
4	16	triphosphate	chemical	The triphosphate moiety at the 5′-end of the tRNA was bonded to the D21-K26 region.	RESULTS
45	49	tRNA	chemical	The triphosphate moiety at the 5′-end of the tRNA was bonded to the D21-K26 region.	RESULTS
68	75	D21-K26	residue_range	The triphosphate moiety at the 5′-end of the tRNA was bonded to the D21-K26 region.	RESULTS
6	16	phosphates	chemical	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
27	41	coordinated to	bond_interaction	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
69	73	Mg2+	chemical	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
75	79	Mg2+	chemical	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
85	89	Mg2+	chemical	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
184	190	CaThg1	protein	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
195	201	HsThg1	protein	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
202	212	structures	evidence	These phosphates were also coordinated to two metal ions, presumably Mg2+ (Mg2+A and Mg2+B) because they were observed at the same positions (figs. S3 and S4) previously identified by CaThg1 and HsThg1 structures.	RESULTS
24	38	coordinated by	bond_interaction	These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A).	RESULTS
73	76	D21	residue_name_number	These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A).	RESULTS
81	84	D69	residue_name_number	These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A).	RESULTS
109	112	G22	residue_name_number	These ions were in turn coordinated by the O atoms of the side chains of D21 and D69 and the main-chain O of G22 (fig. S3A).	RESULTS
0	8	Mutation	experimental_method	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
12	15	D29	residue_name_number	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
20	23	D76	residue_name_number	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
27	33	HsThg1	protein	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
52	55	D21	residue_name_number	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
60	63	D69	residue_name_number	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
67	72	MaTLP	protein	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
110	113	G−1	residue_name_number	Mutation of D29 and D76 in HsThg1 (corresponding to D21 and D69 of MaTLP) has been shown to markedly decrease G−1 addition activity.	RESULTS
34	37	GTP	chemical	Template-dependent binding of the GTP analog to the MaTLP-ppptRNAPheΔ1 complex	RESULTS
52	70	MaTLP-ppptRNAPheΔ1	complex_assembly	Template-dependent binding of the GTP analog to the MaTLP-ppptRNAPheΔ1 complex	RESULTS
35	44	structure	evidence	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
71	76	MaTLP	protein	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
91	95	tRNA	chemical	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
97	109	ppptRNAPheΔ1	chemical	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
120	123	GTP	chemical	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
132	137	GDPNP	chemical	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
163	170	soaking	experimental_method	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
175	193	MaTLP-ppptRNAPheΔ1	complex_assembly	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
202	209	crystal	evidence	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
235	240	GDPNP	chemical	Here, we successfully obtained the structure of the ternary complex of MaTLP, 5′-activated tRNA (ppptRNAPheΔ1), and the GTP analog (GDPNP) (Fig. 3 and fig. S4) by soaking the MaTLP-ppptRNAPheΔ1 complex crystal in a solution containing GDPNP.	RESULTS
13	22	structure	evidence	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
39	46	guanine	chemical	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
68	73	GDPNP	chemical	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
81	108	Watson-Crick hydrogen bonds	bond_interaction	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
114	117	C72	residue_name_number	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
134	160	base-stacking interactions	bond_interaction	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
166	168	G2	residue_name_number	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
176	180	tRNA	chemical	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
240	247	guanine	chemical	The obtained structure showed that the guanine base of the incoming GDPNP formed Watson-Crick hydrogen bonds with C72 and accompanied base-stacking interactions with G2 of the tRNA (Fig. 3B), whereas no interaction was observed between the guanine base and the enzyme.	RESULTS
31	35	tRNA	chemical	The 5′-end (position 2) of the tRNA moved significantly (Fig. 3C) due to the insertion of GDPNP.	RESULTS
90	95	GDPNP	chemical	The 5′-end (position 2) of the tRNA moved significantly (Fig. 3C) due to the insertion of GDPNP.	RESULTS
18	33	5′-triphosphate	chemical	Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D).	RESULTS
69	72	GTP	chemical	Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D).	RESULTS
73	76	ATP	chemical	Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D).	RESULTS
77	89	triphosphate	chemical	Surprisingly, the 5′-triphosphate moiety after movement occupied the GTP/ATP triphosphate position during the activation step (Fig. 3D).	RESULTS
61	64	GTP	chemical	Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs.	RESULTS
116	120	Mg2+	chemical	Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs.	RESULTS
188	197	phosphate	chemical	Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs.	RESULTS
218	227	structure	evidence	Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs.	RESULTS
309	324	reaction center	site	Together with the observation that the 3′-OH of the incoming GTP analog was within coordination distance (2.8 Å) to Mg2+A (fig. S3B) and was able to execute a nucleophilic attack on the α-phosphate of the 5′-end, this structure indicates that the elongation reaction (second reaction) takes place at the same reaction center where the activation reaction (first reaction) occurs.	RESULTS
25	29	tRNA	chemical	Structural change of the tRNA (ppptRNAPheΔ1).	FIG
31	43	ppptRNAPheΔ1	chemical	Structural change of the tRNA (ppptRNAPheΔ1).	FIG
25	29	tRNA	chemical	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
31	43	ppptRNAPheΔ1	chemical	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
45	58	accepter stem	structure_element	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
62	67	MaTLP	protein	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
91	96	GDPNP	chemical	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
102	111	Structure	evidence	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
119	124	GDPNP	chemical	Structural change of the tRNA (ppptRNAPheΔ1) accepter stem in MaTLP caused by insertion of GDPNP. (A) Structure before GDPNP binding.	FIG
4	13	Structure	evidence	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
20	25	GDPNP	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
39	52	Superposition	experimental_method	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
64	74	structures	evidence	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
113	117	tRNA	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
161	166	GDPNP	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
172	185	Superposition	experimental_method	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
207	211	tRNA	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
218	223	GDPNP	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
245	248	GTP	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
299	311	triphosphate	chemical	(B) Structure after GDPNP binding. (C) Superposition of the two structures showing movement of the 5′-end of the tRNA before (blue) and after (red) insertion of GDPNP. (D) Superposition of the 5′-end of the tRNA after GDPNP insertion (red) with GTP at the activation step (green), showing that both triphosphate moieties superpose well.	FIG
4	16	triphosphate	chemical	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
27	32	GDPNP	chemical	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
44	53	interface	site	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
72	73	A	structure_element	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
78	79	B	structure_element	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
147	150	R19	residue_name_number	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
161	162	A	structure_element	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
165	168	R83	residue_name_number	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
179	180	B	structure_element	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
183	186	K86	residue_name_number	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
197	198	B	structure_element	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
205	209	R114	residue_name_number	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
220	221	A	structure_element	The triphosphate moiety of GDPNP was at the interface between molecules A and B and was recognized by the side chains of both molecules, including R19 (molecule A), R83 (molecule B), K86 (molecule B), and R114 (molecule A) (Fig. 3B).	RESULTS
26	40	well conserved	protein_state	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
56	64	mutation	experimental_method	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
94	100	ScThg1	protein	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
102	105	R27	residue_name_number	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
107	110	R93	residue_name_number	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
112	115	K96	residue_name_number	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
121	125	R133	residue_name_number	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
165	168	G−1	residue_name_number	All of these residues are well conserved (fig. S5), and mutation of corresponding residues in ScThg1 (R27, R93, K96, and R133) decreased the catalytic efficiency of G−1 addition.	RESULTS
4	16	triphosphate	chemical	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
24	29	GDPNP	chemical	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
59	63	Mg2+	chemical	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
65	69	Mg2+	chemical	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
87	91	Mg2+	chemical	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
97	101	Mg2+	chemical	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
111	125	coordinated by	bond_interaction	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
130	133	TLP	protein_type	The triphosphate of the GDPNP was also bonded to the third Mg2+ (Mg2+C), which, unlike Mg2+A and Mg2+B, is not coordinated by the TLP molecule (fig. S3B).	RESULTS
5	17	triphosphate	chemical	This triphosphate binding mode is the same as that for the second nucleotide binding site in Thg1.	RESULTS
59	89	second nucleotide binding site	site	This triphosphate binding mode is the same as that for the second nucleotide binding site in Thg1.	RESULTS
93	97	Thg1	protein	This triphosphate binding mode is the same as that for the second nucleotide binding site in Thg1.	RESULTS
54	65	second site	site	However, in previous analyses, the base moiety at the second site was either invisible or far beyond the reaction distance of the phosphate, and therefore, flipping of the base was expected to occur.	RESULTS
130	139	phosphate	chemical	However, in previous analyses, the base moiety at the second site was either invisible or far beyond the reaction distance of the phosphate, and therefore, flipping of the base was expected to occur.	RESULTS
0	35	tRNA binding and repair experiments	experimental_method	tRNA binding and repair experiments of the β-hairpin mutants	RESULTS
43	52	β-hairpin	structure_element	tRNA binding and repair experiments of the β-hairpin mutants	RESULTS
53	60	mutants	protein_state	tRNA binding and repair experiments of the β-hairpin mutants	RESULTS
11	15	tRNA	chemical	To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region.	RESULTS
35	44	β-hairpin	structure_element	To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region.	RESULTS
49	74	created mutation variants	experimental_method	To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region.	RESULTS
104	113	β-hairpin	structure_element	To confirm tRNA recognition by the β-hairpin, we created mutation variants with altered residues in the β-hairpin region.	RESULTS
6	57	tRNA binding and enzymatic activities were measured	experimental_method	Then, tRNA binding and enzymatic activities were measured.	RESULTS
0	9	β-Hairpin	structure_element	β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6).	RESULTS
10	26	deletion variant	protein_state	β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6).	RESULTS
27	39	delR198-R215	mutant	β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6).	RESULTS
83	92	tRNAPheΔ1	chemical	β-Hairpin deletion variant delR198-R215 almost completely abolished the binding of tRNAPheΔ1 (fig. S6).	RESULTS
41	53	delR198-R215	mutant	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
58	70	delG202-E210	mutant	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
130	139	wild type	protein_state	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
149	158	mutations	experimental_method	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
160	165	N179A	mutant	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
170	175	F174A	mutant	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
176	181	N179A	mutant	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
182	187	R188A	mutant	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
196	222	anticodon recognition site	site	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
241	253	Thg1-tRNAHis	complex_assembly	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
262	271	structure	evidence	Furthermore, the enzymatic activities of delR198-R215 and delG202-E210 were very weak (5.2 and 13.5%, respectively) compared with wild type, whereas mutations (N179A and F174A/N179A/R188A) on the anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] had no effect on the catalytic activity (Fig. 4A).	RESULTS
22	31	tRNAHisΔ1	chemical	Experiments using the tRNAHisΔ1 substrate gave similar results (Fig. 4A).	RESULTS
42	59	crystal structure	evidence	All these results are consistent with the crystal structure and suggest that the β-hairpin plays an important role in anticodon-independent binding of the tRNA substrate.	RESULTS
81	90	β-hairpin	structure_element	All these results are consistent with the crystal structure and suggest that the β-hairpin plays an important role in anticodon-independent binding of the tRNA substrate.	RESULTS
155	159	tRNA	chemical	All these results are consistent with the crystal structure and suggest that the β-hairpin plays an important role in anticodon-independent binding of the tRNA substrate.	RESULTS
16	25	β-hairpin	structure_element	Residues in the β-hairpin are not well conserved, except for R215 (fig. S5).	RESULTS
30	48	not well conserved	protein_state	Residues in the β-hairpin are not well conserved, except for R215 (fig. S5).	RESULTS
61	65	R215	residue_name_number	Residues in the β-hairpin are not well conserved, except for R215 (fig. S5).	RESULTS
0	7	Mutants	protein_state	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
8	13	R215A	mutant	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
18	23	R215A	mutant	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
24	29	S213A	mutant	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
44	64	completely conserved	protein_state	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
65	69	R215	residue_name_number	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
74	81	changed	experimental_method	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
85	92	alanine	residue_name	Mutants R215A and R215A/S213A, in which the completely conserved R215 was changed to alanine, showed a moderate effect on the activity (27.3 and 16.3%, respectively).	RESULTS
37	46	conserved	protein_state	Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition.	RESULTS
47	51	R215	residue_name_number	Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition.	RESULTS
56	78	van der Waals contacts	bond_interaction	Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition.	RESULTS
98	107	β-hairpin	structure_element	Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition.	RESULTS
131	135	tRNA	chemical	Thus, specific interactions with the conserved R215 and van der Waals contacts to residues in the β-hairpin would be important for tRNA recognition.	RESULTS
0	19	Mutational analysis	experimental_method	Mutational analysis of the β-hairpin and anticodon binding region.	FIG
27	36	β-hairpin	structure_element	Mutational analysis of the β-hairpin and anticodon binding region.	FIG
41	65	anticodon binding region	site	Mutational analysis of the β-hairpin and anticodon binding region.	FIG
21	33	ppptRNAPheΔ1	chemical	(A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants.	FIG
38	50	ppptRNAHisΔ1	chemical	(A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants.	FIG
62	65	TLP	protein_type	(A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants.	FIG
66	73	mutants	protein_state	(A) Guanylylation of ppptRNAPheΔ1 and ppptRNAHisΔ1 by various TLP mutants.	FIG
19	29	[α-32P]GTP	chemical	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
31	40	wild-type	protein_state	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
41	46	MaTLP	protein	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
52	64	ppptRNAPheΔ1	chemical	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
105	114	tRNAPheΔ1	chemical	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
116	123	tRNAPhe	chemical	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
129	139	tRNAHisΔ−1	chemical	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
151	154	TLP	protein_type	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
155	162	mutants	protein_state	The activity using [α-32P]GTP, wild-type MaTLP, and ppptRNAPheΔ1 is denoted as 100. (B) Guanylylation of tRNAPheΔ1, tRNAPhe, and tRNAHisΔ−1 by various TLP mutants.	FIG
16	25	tRNAPheΔ1	chemical	The activity to tRNAPheΔ1 is about 10% of ppptRNAPheΔ1.	FIG
42	54	ppptRNAPheΔ1	chemical	The activity to tRNAPheΔ1 is about 10% of ppptRNAPheΔ1.	FIG
56	69	accepter stem	structure_element	Termination of the elongation reaction by measuring the accepter stem	RESULTS
0	4	TLPs	protein_type	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
101	108	tRNAPhe	chemical	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
128	130	G1	residue_name_number	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
137	146	tRNAPheΔ1	chemical	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
165	167	G1	residue_name_number	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
172	174	G2	residue_name_number	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
176	187	tRNAPheΔ1,2	chemical	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
240	247	tRNAPhe	chemical	TLPs catalyze the Watson-Crick template–dependent elongation or repair reaction for 5′-end truncated tRNAPhe substrates lacking G1 only (tRNAPheΔ1), or lacking both G1 and G2 (tRNAPheΔ1,2), whereas they do not show any activity with intact tRNAPhe (thus, repair is unnecessary).	RESULTS
4	7	TLP	protein_type	How TLP distinguishes between tRNAs that need 5′-end repair from ones that do not, or in other words, how the elongation reaction is properly terminated, remains unknown.	RESULTS
30	35	tRNAs	chemical	How TLP distinguishes between tRNAs that need 5′-end repair from ones that do not, or in other words, how the elongation reaction is properly terminated, remains unknown.	RESULTS
12	21	structure	evidence	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
29	47	MaTLP-ppptRNAPheΔ1	complex_assembly	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
75	79	Thg1	protein	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
85	88	TLP	protein_type	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
89	94	dimer	oligomeric_state	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
117	121	tRNA	chemical	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
141	153	elbow region	structure_element	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
161	170	β-hairpin	structure_element	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
183	184	B	structure_element	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
212	213	A	structure_element	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
249	257	flexible	protein_state	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
272	281	β-hairpin	structure_element	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
309	313	tRNA	chemical	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
340	353	accepter stem	structure_element	The present structure of the MaTLP-ppptRNAPheΔ1 complex shows that, unlike Thg1, the TLP dimer binds one molecule of tRNA by recognizing the elbow region by the β-hairpin of molecule B and the 5′-end by molecule A. Therefore, we speculated that the flexible nature of the β-hairpin enables the recognition of tRNA substrates with different accepter stem lengths.	RESULTS
32	65	used computer graphics to examine	experimental_method	To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site.	RESULTS
78	87	β-hairpin	structure_element	To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site.	RESULTS
112	116	tRNA	chemical	To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site.	RESULTS
143	156	accepter stem	structure_element	To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site.	RESULTS
208	221	reaction site	site	To confirm this speculation, we used computer graphics to examine whether the β-hairpin region was able to bind tRNA substrates with different accepter stem lengths when the 5′-end was properly placed in the reaction site.	RESULTS
65	69	tRNA	chemical	When the 5′-end was placed in the reaction site, the body of the tRNA molecule shifted in a manner dependent on the accepter stem length.	RESULTS
116	129	accepter stem	structure_element	When the 5′-end was placed in the reaction site, the body of the tRNA molecule shifted in a manner dependent on the accepter stem length.	RESULTS
4	8	tRNA	chemical	The tRNA body also rotated because of the helical nature of the accepter stem (fig. S7).	RESULTS
64	77	accepter stem	structure_element	The tRNA body also rotated because of the helical nature of the accepter stem (fig. S7).	RESULTS
11	20	structure	evidence	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
37	50	accepter stem	structure_element	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
61	68	tRNAPhe	chemical	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
90	99	β-hairpin	structure_element	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
117	129	elbow region	structure_element	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
139	148	tRNAPheΔ1	chemical	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
153	164	tRNAPheΔ1,2	chemical	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
188	197	β-hairpin	structure_element	This model structure showed that the accepter stem of intact tRNAPhe was too long for the β-hairpin to recognize its elbow region, whereas tRNAPheΔ1 and tRNAPheΔ1,2 were recognized by the β-hairpin region (fig. S7), which is consistent with previous experiments.	RESULTS
28	38	structures	evidence	On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates.	RESULTS
62	65	TLP	protein_type	On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates.	RESULTS
126	139	accepter stem	structure_element	On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates.	RESULTS
150	154	tRNA	chemical	On the basis of these model structures, we concluded that the TLP molecule can properly terminate elongation by measuring the accepter stem length of tRNA substrates.	RESULTS
22	26	tRNA	chemical	Dual binding mode for tRNA repair	RESULTS
12	31	structural analysis	experimental_method	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
55	58	TLP	protein_type	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
63	67	Thg1	protein	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
83	93	tetrameric	oligomeric_state	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
146	151	tRNAs	chemical	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
153	157	Thg1	protein	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
161	169	bound to	protein_state	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
170	177	tRNAHis	chemical	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
183	191	tetramer	oligomeric_state	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
201	204	TLP	protein_type	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
208	216	bound to	protein_state	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
217	224	tRNAPhe	chemical	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
230	235	dimer	oligomeric_state	The present structural analysis revealed that although TLP and Thg1 have a similar tetrameric architecture, they have different binding modes for tRNAs: Thg1 is bound to tRNAHis as a tetramer, whereas TLP is bound to tRNAPhe as a dimer.	RESULTS
23	27	tRNA	chemical	This difference in the tRNA binding modes is closely related to their enzymatic functions.	RESULTS
4	40	tRNAHis-specific G−1 addition enzyme	protein_type	The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis.	RESULTS
41	45	Thg1	protein	The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis.	RESULTS
74	87	accepter stem	structure_element	The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis.	RESULTS
92	101	anticodon	structure_element	The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis.	RESULTS
105	112	tRNAHis	chemical	The tRNAHis-specific G−1 addition enzyme Thg1 needs to recognize both the accepter stem and anticodon of tRNAHis.	RESULTS
4	14	tetrameric	oligomeric_state	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
35	39	Thg1	protein	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
118	122	tRNA	chemical	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
137	139	AB	structure_element	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
140	145	dimer	oligomeric_state	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
161	174	accepter stem	structure_element	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
179	181	CD	structure_element	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
182	187	dimer	oligomeric_state	The tetrameric architecture of the Thg1 molecule allows it to access both regions located at the opposite side of the tRNA molecule [the AB dimer recognizes the accepter stem and CD dimer anticodon ].	RESULTS
33	36	TLP	protein_type	In contrast, the binding mode of TLP corresponds to the anticodon-independent repair reactions of 5′-truncated general tRNAs.	RESULTS
119	124	tRNAs	chemical	In contrast, the binding mode of TLP corresponds to the anticodon-independent repair reactions of 5′-truncated general tRNAs.	RESULTS
131	144	accepter stem	structure_element	This binding mode is also suitable for the correct termination of the elongation or repair reaction by measuring the length of the accepter stem by the flexible β-hairpin.	RESULTS
152	160	flexible	protein_state	This binding mode is also suitable for the correct termination of the elongation or repair reaction by measuring the length of the accepter stem by the flexible β-hairpin.	RESULTS
161	170	β-hairpin	structure_element	This binding mode is also suitable for the correct termination of the elongation or repair reaction by measuring the length of the accepter stem by the flexible β-hairpin.	RESULTS
8	15	tRNAHis	chemical	Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs.	RESULTS
34	43	guanosine	chemical	Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs.	RESULTS
45	48	G−1	residue_name_number	Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs.	RESULTS
142	147	tRNAs	chemical	Because tRNAHis requires an extra guanosine (G−1) at the 5′-end, the repair enzyme has to extend the 5′-end by one more nucleotide than other tRNAs.	RESULTS
0	3	TLP	protein_type	TLP has been shown to confer such catalytic activity on tRNAHisΔ−1 (Fig. 4B).	RESULTS
56	66	tRNAHisΔ−1	chemical	TLP has been shown to confer such catalytic activity on tRNAHisΔ−1 (Fig. 4B).	RESULTS
25	28	TLP	protein_type	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
29	36	mutants	protein_state	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
50	59	β-hairpin	structure_element	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
63	72	truncated	protein_state	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
77	86	tRNAPheΔ1	chemical	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
130	137	tRNAPhe	chemical	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
139	142	GUG	chemical	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
183	186	His	residue_name	Here, we showed that the TLP mutants, wherein the β-hairpin is truncated and tRNAPheΔ1 binding ability is lost, can still bind to tRNAPhe (GUG) whose anticodon is changed to that for His (fig. S6, C, H, and I).	RESULTS
17	24	tRNAPhe	chemical	Also, the intact tRNAPhe, which is not recognized by TLP (Fig. 4B and fig. S6E), can be recognized when its anticodon is changed to that for His (fig. S6D).	RESULTS
53	56	TLP	protein_type	Also, the intact tRNAPhe, which is not recognized by TLP (Fig. 4B and fig. S6E), can be recognized when its anticodon is changed to that for His (fig. S6D).	RESULTS
141	144	His	residue_name	Also, the intact tRNAPhe, which is not recognized by TLP (Fig. 4B and fig. S6E), can be recognized when its anticodon is changed to that for His (fig. S6D).	RESULTS
17	20	TLP	protein_type	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
21	28	variant	protein_state	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
30	35	F174A	mutant	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
36	41	N179A	mutant	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
42	47	R188A	mutant	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
55	81	anticodon recognition site	site	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
100	112	Thg1-tRNAHis	complex_assembly	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
121	130	structure	evidence	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
201	211	tRNAHisΔ−1	chemical	Furthermore, the TLP variant (F174A/N179A/R188A) whose anticodon recognition site [deduced from the Thg1-tRNAHis complex structure ] is disrupted has been shown to have a reduced catalytic activity to tRNAHisΔ−1 (Fig. 4B).	RESULTS
45	48	TLP	protein_type	All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis.	RESULTS
70	75	tRNAs	chemical	All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis.	RESULTS
89	92	His	residue_name	All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis.	RESULTS
124	128	Thg1	protein	All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis.	RESULTS
140	147	tRNAHis	chemical	All these experimental results indicate that TLP recognizes and binds tRNAs carrying the His anticodon in the same way that Thg1 recognizes tRNAHis.	RESULTS
24	27	TLP	protein_type	Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon.	RESULTS
36	40	tRNA	chemical	Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon.	RESULTS
118	131	accepter stem	structure_element	Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon.	RESULTS
140	149	anticodon	structure_element	Thus, we concluded that TLP has two tRNA binding modes that are selectively used, depending on both the length of the accepter stem and the anticodon.	RESULTS
103	106	His	residue_name	The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction.	RESULTS
129	132	TLP	protein_type	The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction.	RESULTS
143	147	tRNA	chemical	The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction.	RESULTS
211	214	G−1	residue_name_number	The elongation or repair reaction normally terminates when the 5′-end reaches position 1, but when the His anticodon is present, TLP binds the tRNA in the second mode by recognizing the anticodon to execute the G−1 addition reaction.	RESULTS
39	42	TLP	protein_type	By having two different binding modes, TLP can manage this special feature of tRNAHis.	RESULTS
78	85	tRNAHis	chemical	By having two different binding modes, TLP can manage this special feature of tRNAHis.	RESULTS
4	8	Thg1	protein	The Thg1/TLP family of proteins extends tRNA chains in the 3′-5′ direction.	DISCUSS
9	12	TLP	protein_type	The Thg1/TLP family of proteins extends tRNA chains in the 3′-5′ direction.	DISCUSS
40	44	tRNA	chemical	The Thg1/TLP family of proteins extends tRNA chains in the 3′-5′ direction.	DISCUSS
11	23	5′-phosphate	chemical	First, the 5′-phosphate is activated by GTP/ATP.	DISCUSS
40	43	GTP	chemical	First, the 5′-phosphate is activated by GTP/ATP.	DISCUSS
44	47	ATP	chemical	First, the 5′-phosphate is activated by GTP/ATP.	DISCUSS
20	29	phosphate	chemical	Then, the activated phosphate is attacked by the incoming nucleotide, resulting in an extension by one nucleotide at the 5′-end.	DISCUSS
22	28	solved	experimental_method	Here, we successfully solved for the first time the intermediate structures of the template-dependent 3′-5′ elongation complex of MaTLP.	DISCUSS
65	75	structures	evidence	Here, we successfully solved for the first time the intermediate structures of the template-dependent 3′-5′ elongation complex of MaTLP.	DISCUSS
130	135	MaTLP	protein	Here, we successfully solved for the first time the intermediate structures of the template-dependent 3′-5′ elongation complex of MaTLP.	DISCUSS
22	32	structures	evidence	On the basis of these structures, we will discuss the 3′-5′ addition reaction compared with canonical 5′-3′ elongation by DNA/RNA polymerases.	DISCUSS
122	141	DNA/RNA polymerases	protein_type	On the basis of these structures, we will discuss the 3′-5′ addition reaction compared with canonical 5′-3′ elongation by DNA/RNA polymerases.	DISCUSS
66	69	TLP	protein_type	Figure 5 is a schematic diagram of the 3′-5′ addition reaction of TLP.	DISCUSS
20	46	triphosphate binding sites	site	This enzyme has two triphosphate binding sites and one reaction center at the position overlapping these two binding sites (Fig. 5A).	DISCUSS
55	70	reaction center	site	This enzyme has two triphosphate binding sites and one reaction center at the position overlapping these two binding sites (Fig. 5A).	DISCUSS
109	122	binding sites	site	This enzyme has two triphosphate binding sites and one reaction center at the position overlapping these two binding sites (Fig. 5A).	DISCUSS
35	38	GTP	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
39	42	ATP	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
46	54	bound to	protein_state	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
55	61	site 1	site	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
77	89	5′-phosphate	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
97	101	tRNA	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
121	125	Mg2+	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
145	154	phosphate	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
162	165	GTP	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
166	169	ATP	chemical	In the first activation step, when GTP/ATP is bound to site 1 (Fig. 5B), the 5′-phosphate of the tRNA is deprotonated by Mg2+A and attacks the α-phosphate of the GTP/ATP, resulting in an activated intermediate (Fig. 5C).	DISCUSS
4	13	structure	evidence	The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate.	DISCUSS
21	39	MaTLP-ppptRNAPheΔ1	complex_assembly	The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate.	DISCUSS
66	76	phosphates	chemical	The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate.	DISCUSS
77	92	coordinate with	bond_interaction	The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate.	DISCUSS
93	97	Mg2+	chemical	The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate.	DISCUSS
103	107	Mg2+	chemical	The structure of the MaTLP-ppptRNAPheΔ1 complex, wherein β- and γ-phosphates coordinate with Mg2+A and Mg2+B, respectively (Figs. 3A and 5C′), may represent this activated intermediate.	DISCUSS
34	44	nucleotide	chemical	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
48	54	site 2	site	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
84	106	Watson-Crick base pair	bond_interaction	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
114	124	nucleotide	chemical	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
182	192	nucleotide	chemical	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
229	233	Mg2+	chemical	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
243	258	5′-triphosphate	chemical	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
266	270	tRNA	chemical	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
278	293	reaction center	site	Subsequent binding of an incoming nucleotide to site 2 followed by formation of the Watson-Crick base pair with a nucleotide in the template strand conveys the 3′-OH of the incoming nucleotide to the position of deprotonation by Mg2+A and the 5′-triphosphate of the tRNA to the reaction center (Figs. 3B and 5D).	DISCUSS
18	27	structure	evidence	Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion.	DISCUSS
44	67	3′-5′ elongation enzyme	protein_type	Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion.	DISCUSS
79	94	reaction center	site	Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion.	DISCUSS
117	141	5′-3′ elongation enzymes	protein_type	Thus, the present structure shows that this 3′-5′ elongation enzyme utilizes a reaction center homologous to that of 5′-3′ elongation enzymes for both activation and elongation in a stepwise fashion.	DISCUSS
24	27	TLP	protein_type	It should be noted that TLP has evolved to allow the occurrence of these two elaborate reaction steps within one reaction center.	DISCUSS
113	128	reaction center	site	It should be noted that TLP has evolved to allow the occurrence of these two elaborate reaction steps within one reaction center.	DISCUSS
8	23	reaction center	site	(A) The reaction center overlapped with two triphosphate binding sites.	FIG
44	70	triphosphate binding sites	site	(A) The reaction center overlapped with two triphosphate binding sites.	FIG
33	46	binding sites	site	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
51	55	Mg2+	chemical	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
58	62	Mg2+	chemical	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
69	73	Mg2+	chemical	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
76	77	P	site	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
103	126	phosphate binding sites	site	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
147	159	binding site	site	A, B, and C (in green) represent binding sites for Mg2+A, Mg2+B, and Mg2+C. P (in blue) represents the phosphate binding sites; O− (in red) is the binding site for the deprotonated OH group.	FIG
10	13	TLP	protein_type	Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8).	FIG
27	31	tRNA	chemical	Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8).	FIG
36	40	Mg2+	chemical	Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8).	FIG
69	78	Structure	evidence	Important TLP residues for tRNA and Mg2+ binding are also shown. (B) Structure of the activation complex (corresponding to fig. S8).	FIG
0	3	GTP	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
4	7	ATP	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
17	44	triphosphate binding site 1	site	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
79	91	5′-phosphate	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
106	115	phosphate	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
119	122	GTP	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
123	126	ATP	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
132	135	PPi	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
137	160	inorganic pyrophosphate	chemical	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
188	197	structure	evidence	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
246	255	structure	evidence	GTP/ATP binds to triphosphate binding site 1; the deprotonated OH group of the 5′-phosphate attacks the α-phosphate of GTP/ATP, and PPi (inorganic pyrophosphate) is released. (C) Possible structure after the activation step as suggested from the structure of (C′).	FIG
5	14	Structure	evidence	(C′) Structure before the elongation reaction (corresponding to Fig. 3A).	FIG
4	19	5′-triphosphate	chemical	The 5′-triphosphate of the tRNA binds to the same site as for activation of the 5′-terminus of the tRNA in (B).	FIG
27	31	tRNA	chemical	The 5′-triphosphate of the tRNA binds to the same site as for activation of the 5′-terminus of the tRNA in (B).	FIG
99	103	tRNA	chemical	The 5′-triphosphate of the tRNA binds to the same site as for activation of the 5′-terminus of the tRNA in (B).	FIG
4	13	Structure	evidence	(D) Structure of initiation of the elongation reaction (corresponding to Fig. 3B).	FIG
25	28	GTP	chemical	The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2).	FIG
37	63	Watson-Crick hydrogen bond	bond_interaction	The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2).	FIG
73	83	nucleotide	chemical	The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2).	FIG
96	98	72	residue_number	The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2).	FIG
127	152	base-stacking interaction	bond_interaction	The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2).	FIG
178	180	G2	residue_name_number	The base of the incoming GTP forms a Watson-Crick hydrogen bond with the nucleotide at position 72 in the template chain and a base-stacking interaction with a neighboring base (G2).	FIG
45	60	5′-triphosphate	chemical	Movement of the 5′-terminal chain leaves the 5′-triphosphate of the tRNA in the same site as the activation step in (B).	FIG
68	72	tRNA	chemical	Movement of the 5′-terminal chain leaves the 5′-triphosphate of the tRNA in the same site as the activation step in (B).	FIG
26	29	GTP	chemical	The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction.	FIG
49	53	Mg2+	chemical	The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction.	FIG
73	82	phosphate	chemical	The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction.	FIG
147	159	triphosphate	chemical	The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction.	FIG
171	181	nucleotide	chemical	The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction.	FIG
195	201	site 1	site	The 3′-OH of the incoming GTP is deprotonated by Mg2+A and attacks the α-phosphate to form a covalent bond. (E) After the elongation reaction, the triphosphate of the new nucleotide is placed on site 1, as in (C′), and is ready for the next reaction.	FIG
137	152	reaction center	site	Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core.	DISCUSS
165	169	Mg2+	chemical	Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core.	DISCUSS
175	179	Mg2+	chemical	Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core.	DISCUSS
188	197	conserved	protein_state	Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core.	DISCUSS
198	212	catalytic core	site	Figure 6 compares the 3′-5′ and 5′-3′ elongation mechanisms, showing the symmetrical nature of both elongation reactions using a similar reaction center composed of Mg2+A and Mg2+B in the conserved catalytic core.	DISCUSS
3	6	TLP	protein_type	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
106	115	phosphate	chemical	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
123	127	tRNA	chemical	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
174	191	T7 RNA polymerase	protein	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
210	234	5′-3′ DNA/RNA polymerase	protein_type	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
283	286	RNA	chemical	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
309	318	phosphate	chemical	In TLP, which carries out 3′-5′ elongation, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the T7 RNA polymerase, a representative 5′-3′ DNA/RNA polymerase, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	DISCUSS
41	43	Mg	chemical	In these reactions, the roles of the two Mg ions are identical.	DISCUSS
0	4	Mg2+	chemical	Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase.	DISCUSS
56	59	TLP	protein_type	Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase.	DISCUSS
95	98	RNA	chemical	Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase.	DISCUSS
108	125	T7 RNA polymerase	protein	Mg2+A activates the 3′-OH of the incoming nucleotide in TLP and the 3′-OH of the 3′-end of the RNA chain in T7 RNA polymerase.	DISCUSS
12	16	Mg2+	chemical	The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase.	DISCUSS
37	52	5′-triphosphate	chemical	The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase.	DISCUSS
60	64	tRNA	chemical	The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase.	DISCUSS
68	71	TLP	protein_type	The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase.	DISCUSS
103	120	T7 RNA polymerase	protein	The role of Mg2+B is to position the 5′-triphosphate of the tRNA in TLP and the incoming nucleotide in T7 RNA polymerase.	DISCUSS
10	14	Mg2+	chemical	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
24	38	coordinated by	bond_interaction	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
41	50	conserved	protein_state	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
51	54	Asp	residue_name	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
56	59	D21	residue_name_number	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
64	67	D69	residue_name_number	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
71	74	TLP	protein_type	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
83	92	conserved	protein_state	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
93	107	catalytic core	site	These two Mg2+ ions are coordinated by a conserved Asp (D21 and D69 in TLP) in the conserved catalytic core.	DISCUSS
0	10	Structures	evidence	Structures of template-dependent nucleotide elongation in the 3′-5′ and 5′-3′ directions.	FIG
53	56	TLP	protein_type	Symmetrical relationship between 3′-5′ elongation by TLP (this study) (left) and 5′-3′ elongation by T7 RNA polymerase [Protein Data Bank (PDB) ID: 1S76] (right).	FIG
101	118	T7 RNA polymerase	protein	Symmetrical relationship between 3′-5′ elongation by TLP (this study) (left) and 5′-3′ elongation by T7 RNA polymerase [Protein Data Bank (PDB) ID: 1S76] (right).	FIG
96	105	phosphate	chemical	In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	FIG
113	117	tRNA	chemical	In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	FIG
238	241	RNA	chemical	In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	FIG
264	273	phosphate	chemical	In the 3′-5′ elongation reaction, the 3′-OH of the incoming nucleotide attacks the 5′-activated phosphate of the tRNA to form a phosphodiester bond, whereas in the 5′-3′ elongation reaction, the 3′-OH of the 3′-terminal nucleotide of the RNA attacks the activated phosphate of the incoming nucleotide to form a phosphodiester bond.	FIG
24	28	Mg2+	chemical	Green spheres represent Mg2+ ions.	FIG
30	34	tRNA	chemical	Because the chemical roles of tRNA and the incoming nucleotide are reversed in these two reactions, these two substrates are inserted into a similar reaction center from opposite directions (Fig. 6).	DISCUSS
149	164	reaction center	site	Because the chemical roles of tRNA and the incoming nucleotide are reversed in these two reactions, these two substrates are inserted into a similar reaction center from opposite directions (Fig. 6).	DISCUSS
164	183	DNA/RNA polymerases	protein_type	However, from an energetic viewpoint, these two reactions are clearly different: Whereas the high energy of the incoming nucleotide is used for its own addition in DNA/RNA polymerases, the high energy of the incoming nucleotide is used for subsequent addition in TLP.	DISCUSS
263	266	TLP	protein_type	However, from an energetic viewpoint, these two reactions are clearly different: Whereas the high energy of the incoming nucleotide is used for its own addition in DNA/RNA polymerases, the high energy of the incoming nucleotide is used for subsequent addition in TLP.	DISCUSS
17	20	TLP	protein_type	For this reason, TLP requires a mechanism that activates the 5′-terminus of the tRNA during the initial step of the reaction.	DISCUSS
80	84	tRNA	chemical	For this reason, TLP requires a mechanism that activates the 5′-terminus of the tRNA during the initial step of the reaction.	DISCUSS
110	125	reaction center	site	Our analysis showed that the initial activation and subsequent elongation reactions occur sequentially at one reaction center.	DISCUSS
45	68	substrate binding sites	site	In this case, the enzyme needs to create two substrate binding sites for two different reactions in the vicinities of one reaction center.	DISCUSS
122	137	reaction center	site	In this case, the enzyme needs to create two substrate binding sites for two different reactions in the vicinities of one reaction center.	DISCUSS
0	3	TLP	protein_type	TLP has successfully created such sites by utilizing a conformational change in the tRNA through Watson-Crick base pairing (Fig. 3).	DISCUSS
84	88	tRNA	chemical	TLP has successfully created such sites by utilizing a conformational change in the tRNA through Watson-Crick base pairing (Fig. 3).	DISCUSS
97	122	Watson-Crick base pairing	bond_interaction	TLP has successfully created such sites by utilizing a conformational change in the tRNA through Watson-Crick base pairing (Fig. 3).	DISCUSS
33	36	TLP	protein_type	These structural features of the TLP molecule suggest that development of an activation reaction site is a prerequisite for developing the 3′-5′ elongation enzyme.	DISCUSS
77	101	activation reaction site	site	These structural features of the TLP molecule suggest that development of an activation reaction site is a prerequisite for developing the 3′-5′ elongation enzyme.	DISCUSS
139	162	3′-5′ elongation enzyme	protein_type	These structural features of the TLP molecule suggest that development of an activation reaction site is a prerequisite for developing the 3′-5′ elongation enzyme.	DISCUSS
51	74	5′-3′ elongation enzyme	protein_type	This is clearly more difficult than developing the 5′-3′ elongation enzyme, wherein the activation reaction site is not necessary, and which may be the primary reason why the 5′-3′ elongation enzyme has been exclusively developed.	DISCUSS
88	112	activation reaction site	site	This is clearly more difficult than developing the 5′-3′ elongation enzyme, wherein the activation reaction site is not necessary, and which may be the primary reason why the 5′-3′ elongation enzyme has been exclusively developed.	DISCUSS
175	198	5′-3′ elongation enzyme	protein_type	This is clearly more difficult than developing the 5′-3′ elongation enzyme, wherein the activation reaction site is not necessary, and which may be the primary reason why the 5′-3′ elongation enzyme has been exclusively developed.	DISCUSS
88	91	TLP	protein_type	Here, we established a structural basis for 3′-5′ nucleotide elongation and showed that TLP has evolved to acquire a two-step Watson-Crick template–dependent 3′-5′ elongation reaction using the catalytic center homologous to 5′-3′ elongation enzymes.	DISCUSS
194	210	catalytic center	site	Here, we established a structural basis for 3′-5′ nucleotide elongation and showed that TLP has evolved to acquire a two-step Watson-Crick template–dependent 3′-5′ elongation reaction using the catalytic center homologous to 5′-3′ elongation enzymes.	DISCUSS
225	249	5′-3′ elongation enzymes	protein_type	Here, we established a structural basis for 3′-5′ nucleotide elongation and showed that TLP has evolved to acquire a two-step Watson-Crick template–dependent 3′-5′ elongation reaction using the catalytic center homologous to 5′-3′ elongation enzymes.	DISCUSS
4	15	active site	site	The active site of this enzyme is created at the dimerization interface.	DISCUSS
49	71	dimerization interface	site	The active site of this enzyme is created at the dimerization interface.	DISCUSS
88	101	accepter stem	structure_element	The dimerization also endows this protein with the ability to measure the length of the accepter stem of the tRNA substrate, so that the enzyme can properly terminate the elongation reaction.	DISCUSS
109	113	tRNA	chemical	The dimerization also endows this protein with the ability to measure the length of the accepter stem of the tRNA substrate, so that the enzyme can properly terminate the elongation reaction.	DISCUSS
97	100	G−1	residue_name_number	Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers).	DISCUSS
113	120	tRNAHis	chemical	Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers).	DISCUSS
149	154	dimer	oligomeric_state	Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers).	DISCUSS
158	164	dimers	oligomeric_state	Furthermore, the dual binding mode of this protein suggests that it has further evolved to cover G−1 addition of tRNAHis by additional dimerization (dimer of dimers).	DISCUSS
18	37	structural analysis	experimental_method	Thus, the present structural analysis is consistent with the scenario in which TLP began as a 5′-end repair enzyme and evolved into a tRNAHis-specific G−1 addition enzyme.	DISCUSS
79	82	TLP	protein_type	Thus, the present structural analysis is consistent with the scenario in which TLP began as a 5′-end repair enzyme and evolved into a tRNAHis-specific G−1 addition enzyme.	DISCUSS
134	170	tRNAHis-specific G−1 addition enzyme	protein_type	Thus, the present structural analysis is consistent with the scenario in which TLP began as a 5′-end repair enzyme and evolved into a tRNAHis-specific G−1 addition enzyme.	DISCUSS
40	44	Thg1	protein	The detailed molecular mechanism of the Thg1/TLP family established by our analysis will open up new perspectives in our understanding of 3′-5′ versus 5′-3′ polymerization and the molecular evolution of template-dependent polymerases.	DISCUSS
45	48	TLP	protein_type	The detailed molecular mechanism of the Thg1/TLP family established by our analysis will open up new perspectives in our understanding of 3′-5′ versus 5′-3′ polymerization and the molecular evolution of template-dependent polymerases.	DISCUSS
203	233	template-dependent polymerases	protein_type	The detailed molecular mechanism of the Thg1/TLP family established by our analysis will open up new perspectives in our understanding of 3′-5′ versus 5′-3′ polymerization and the molecular evolution of template-dependent polymerases.	DISCUSS
12	17	tRNAs	chemical	Transcribed tRNAs were purified by a HiTrap DEAE FF column (GE Healthcare) as previously described.	METHODS
7	12	tRNAs	chemical	Pooled tRNAs were precipitated with isopropanol and dissolved in buffer E [20 mM Hepes-NaOH (pH 7.5), 100 mM NaCl, and 10 mM MgCl2].	METHODS
49	54	Thg1p	protein	The highly conserved tRNAHis guanylyltransferase Thg1p interacts with the origin recognition complex and is required for the G2/M phase transition in the yeast Saccharomyces cerevisiae	REF