SII-SWORD/CoKE huggingface dataset:
Photosystem II cytochrome b559, conserved site (PSII_cyt_b559_CS)
Type: Conserved_site

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This family represents cytochrome b559, which forms part of the reaction centre core of PSII as a heterodimer composed of one alpha subunit (PsbE), one beta (PsbF) subunit, and a haem cofactor. Two histidine residues from each subunit coordinate the haem. Although cytochrome b559 is a redox-active protein, it is unlikely to be involved in the primary electron transport in PSII due to its very slow photo-oxidation and photo-reduction kinetics. Instead, cytochrome b559 could participate in a secondary electron transport pathway that helps protect PSII from photo-damage. Cytochrome b559 is essential for PSII assembly .
Photosystem II cytochrome b559, alpha subunit (PSII_cyt_b559_asu)
Type: Family

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This family represents the alpha subunit (PsbE) of cytochrome b559, which forms a haem-binding heterodimer with the beta subunit (PsbF) (

) within the reaction centre core of PSII. Both PsbE and PsbF are essential components for PSII assembly, and are probably involved in secondary electron transport mechanisms that help to protect PSII from photo-damage .
DAHP synthase, class 1 (DAHP_synth_1)
Type: Family

Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (

). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids.

DAHP synthetases fall into two classes, class I (represented by this entry) and class II. Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme .

The three-dimentional structures of DAHP synthases have been determined . The DAHPS(Phe) monomer is a (β/α)8 barrel with an additional N-terminal β strand and helices and an extra β sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site .

The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.

This entry also includes phospho-2-dehydro-3-deoxyheptonate aldolase AMT16 from the Alternaria rot fungus. AMT16 is a component required for the non-ribosomal biosynthesis of the cyclic depsipeptides known as AM-toxins. The exact role of AMT16 is not known .
Anthranilate synthase/para-aminobenzoate synthase like domain (TrpG/PapA_dom)
Type: Domain

This entry represents the anthranilate synthase/para-aminobenzoate synthase domain, which share sequence similarity to the glutamine amidotransferase domain

. Anthranilate synthase play a role in the tryptophan-biosynthetic pathway, while the para-aminobenzoate synthase is involved in the folate biosynthetic pathway. In at least one case, a single polypeptide from Bacillus subtilis was shown to have both functions.

This entry contains proteins similar to para-aminobenzoate (PABA) synthase and ASase. These enzymes catalyze similar reactions and produce similar products, PABA and ortho-aminobenzoate (anthranilate). Each enzyme is composed of non-identical subunits: a glutamine amidotransferase subunit (component II) and a subunit that produces an aminobenzoate products (component I). ASase catalyses the synthesis of anthranilate from chorismate and glutamine and is a tetrameric protein comprising two copies each of components I and II. Component II of ASase belongs to the family of triad GTases which hydrolyse glutamine and transfer nascent ammonia between the active sites. In some bacteria, such as Escherichia coli, component II can be much larger than in other organisms, due to the presence of phosphoribosyl-anthranilate transferase (PRTase) activity. PRTase catalyses the second step in tryptophan biosynthesis and results in the addition of 5-phosphoribosyl-1-pyrophosphate to anthranilate to create N-5'-phosphoribosyl-anthranilate. In E.coli, the first step in the conversion of chorismate to PABA involves two proteins: PabA and PabB which co-operate to transfer the amide nitrogen of glutamine to chorismate forming 4-amino-4 deoxychorismate (ADC). PabA acts as a glutamine amidotransferase, supplying an amino group to PabB, which carries out the amination reaction. A third protein PabC then mediates elimination of pyruvate and aromatisation to give PABA. Several organisms have bipartite proteins containing fused domains homologous to PabA and PabB commonly called PABA synthases. These hybrid PABA synthases may produce ADC and not PABA. .
Aminomethyltransferase, folate-binding domain (GcvT_N)
Type: Domain

This entry represents the N-terminal in glycine cleavage T-proteins, which are part of the glycine cleavage multienzyme complex (GcvT) found in bacteria and the mitochondria of eukaryotes. This domain is also found in YgfZ proteins. This domain represents a possible folate-binding domain. Trimethylamine-oxide aldolase is also represented by this entry; it catalyses the conversion of trimethylamine N-oxide (TMAO) to dimethylamine (DMA) and formaldehyde .

The glycine cleavage multienzyme complex (GCV) catalyses the catabolism of glycine in eukaryotes. GcvT (aminomethyltransferase,

) is a folate-dependent enzyme that catalyses the release of ammonia and the transfer of the methylene carbon unit (C1 unit) to tetrahydrofolate (H4folate) from the aminomethyl intermediate attached to the lipoate cofactor of H-protein . GCV is found in bacteria and the mitochondria of eukaryotes. Mutations in the human GcvT gene are known to cause nonketotic hyperglycinemia .
Glycine cleavage system T protein (GcvT)
Type: Family

This entry represents aminomethyltransferases GcvT, part of the glycine cleavage multienzyme complex (GCV).

The glycine cleavage multienzyme complex (GCV) catalyses the catabolism of glycine in eukaryotes. GcvT (aminomethyltransferase,

) is a folate-dependent enzyme that catalyses the release of ammonia and the transfer of the methylene carbon unit (C1 unit) to tetrahydrofolate (H4folate) from the aminomethyl intermediate attached to the lipoate cofactor of H-protein . GCV is found in bacteria and the mitochondria of eukaryotes. Mutations in the human GcvT gene are known to cause nonketotic hyperglycinemia .
Pseudouridine synthase, RluA-like, conserved site (PsdUridine_synth_RluA-like_CS)
Type: Conserved_site

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are :

Pseudouridine synthase I, TruA.

Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.

Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.

Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.

Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.

This entry represents a conserved region located in the central part of a group of pseudouridine synthases, predominantly those that belong to the RluA subfamily of pseudouridine synthases, including RluA, RluC, RluD and TruC. These homologous enzymes synthesize pseudouridine from uracil in specific positions . RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis . RluA shows an elongated, mixed α/β fold, with an with an eight-stranded β-sheet core and additional β-strands, α-helices and loops . Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different .
Pseudouridine synthase, RluC/RluD (PsdUridine_synth_RluC/D)
Type: Family

This entry represents the RluC/RluD subfamily of pseudouridine synthases. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases uracil-955, U-2504, and U-2580 in the case of RluC and uracil-1911, U-1915, and U-1917 in the case of RluD . RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis . Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different.

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are :

Pseudouridine synthase I, TruA.

Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.

Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.

Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.

Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.
PIN domain toxin (Mtu_PIN)
Type: Family

Members of this family are VapC proteins that consist almost entirely of a PIN (PilT N terminus) domain. This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis, but additional members are found now Synechococcus sp. WH8102, etc. This family includes ribonucleases VapC24 and Vap25 among others. They are the toxic component of a toxin-antitoxin (TA) module. They act as an RNase and all their toxic effects are neutralised by coexpression with cognate antitoxin .
Polycystin cation channel (Polycystin_cat)
Type: Domain

This represents the N-terminal region of polycystin, a member of the Polycystin Cation Channel (PCC) family. Polycystin is a huge protein of 4303aa. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative transmembrane regions in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na
+
, K
+
and Ca
2+
) channel that is activated by Ca
2+
. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects .
Protein MutL (MutL)
Type: Family

This small family includes GlmL/MutL from Clostridium tetanomorphum and Clostridium cochlearium. GlmL is located between the genes for the two subunits, epsilon (GlmE) and sigma (GlmS), of the coenzyme-B12-dependent glutamate mutase (methylaspartate mutase), the first enzyme in a pathway of glutamate fermentation. Members shows significant sequence similarity to the hydantoinase branch of the hydantoinase/oxoprolinase family .
Malate:quinone-oxidoreductase (MQO)
Type: Family

The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in Escherichia coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase .
Sucrose-6-phosphate hydrolase (Suc6P_hydrolase)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 32 comprises enzymes with several known activities; invertase (

); inulinase; levanase (

); exo-inulinase (

); sucrose:sucrose 1-fructosyltransferase (

); and fructan:fructan 1-fructosyltransferase (

). This subfamily represents sucrose-6-phosphate hydrolase (invertase).
Cystathionine beta-lyase, bacterial (Cys_b_lyase_bac)
Type: Family

Cystathionine beta-lyase (alternate name: beta-cystathionase) is one of several pyridoxal-dependent enzymes of cysteine, methionine, and homocysteine metabolism. This enzyme is involved in the biosynthesis of Met from Cys .
O-succinylhomoserine sulfhydrylase (O-succ-hSer_sulfhydrylase)
Type: Family

These sequences represent O-succinylhomoserine sulfhydrylase, one of several related pyridoxal phosphate-dependent enzymes of cysteine and methionine metabolism. This enzyme is part of an alternative pathway of homocysteine biosynthesis, a step in methionine biosynthesis.
O-acetylhomoserine/O-acetylserine sulfhydrylase (OAc-hSer/O-AcSer_sulfhydrylase)
Type: Family

This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH,

) and O-acetylserine sulfhydrylase (OAS,

) . An alternate name for OAH sulfhydrylase is homocysteine synthase.

This family also includes sulfhydrylase FUB7, which is part of the gene cluster that mediates the biosynthesis of fusaric acid , and Sulfhydrylase-like protein lolC1/2, associated with the biosynthesis of loline alkaloids, potent insecticidal agents composed of a pyrrolizidine ring system and an uncommon ether bridge linking carbons 2 and 7 .
D-3-phosphoglycerate dehydrogenase (PGDH)
Type: Family

Phosphoglycerate dehydrogenases (PGDH) have at least two different structural domains: the nucleotide binding and the substrate binding. There are three types of PGDH: type 3 enzymes are composed only of these two domains, type2 enzymes contain an extra C-terminal regulatory domain (ACT domain), type 1 enzymes contain both the regulatory domain and an extra allosteric domain . This entry represents the type 1 enzyme. Interestingly, this type of PGDH is found in bacteria such as Mycobacterium, Bacillus subtilis, Corynebacterium, plants such as Arabidopsis, and higher order eukaryotes, including mammals. The PGDHs from E. coli and some lower eukaryotes, such as yeast and Neurospora, belong to the type2 PGDH and are not included in this entry .
L-methionine gamma-lyase (L-Met_gamma_lys)
Type: Family

This family of sequences is a methionine gamma-lyase subset of a family of PLP-dependent trans-sulphuration enzymes. The member from the parasite Trichomonas vaginalis is described as catalyzing alpha gamma- and alpha-beta eliminations and gamma-replacement reactions on methionine, cysteine, and some derivatives . This entry also includes Pseudomonas putida mdeA, which is a L-methionine gamma-lyase .
Cystathionine beta-lyase, eukaryotic (Cys_b_lyase_euk)
Type: Family

This group of sequences represent cystathionine beta-lyase (alternate name: beta-cystathionase), one of several pyridoxal-dependent enzymes of cysteine, methionine, and homocysteine metabolism. This enzyme is involved in the biosynthesis of Met from Cys.
3(2),5 -bisphosphate nucleotidase (DPNP)
Type: Family

Sulphate is incorporated into 3-phosphoadenylylsulphate, PAPS, for utilization in pathways such as methionine biosynthesis. Transfer of sulphate from PAPS to an acceptor leaves adenosine 3'-5'-bisphosphate, APS. In plants these sequences represent a form of the enzyme, 3'(2'),5'-bisphosphate nucleotidase, which removes the 3'-phosphate from APS to regenerate AMP and help drive the cycle. Sensitivity of this essential enzyme to sodium and other metal ions results is responsible for characterisation of this enzyme as a salt tolerance protein . Some members of this family are active also as inositol 1-monophosphatase .
3'(2'),5'-bisphosphate nucleotidase CysQ (CysQ)
Type: Family

This entry represents CysQ, a 3'-nucleotidase that converts adenosine-3',5'-bisphosphate (PAP) to AMP . It may also convert adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS) . CysQ contains a conserved sequence motif, D(X)n EE(X)nDP(I/L)D(S/G/A)T(X)nWD(X)11GG, required for metal ion coordination. It has been found to be inhibited by lithium and calcium in vitro and is a main target of lithium toxicity in vivo .
Photosystem II cytochrome b559, beta subunit (PSII_cyt_b559_bsu)
Type: Family

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This family represents the beta subunit (PsbF) of cytochrome b559, which forms a haem-binding heterodimer with the alpha subunit (PsbE) (

) within the reaction centre core of PSII. Both PsbE and PsbF are essential components for PSII assembly, and are probably involved in secondary electron transport mechanisms that help to protect PSII from photo-damage .