SII-SWORD/CoKE huggingface dataset:
Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (A-D-PHexomutase_a/b/a-I)
Type: Domain

This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer α/β/α topology.

The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (

) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (

;

) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (

) and PAGM (

) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Alpha-D-phosphohexomutase, alpha/beta/alpha domain II (A-D-PHexomutase_a/b/a-II)
Type: Domain

This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer α/β/α topology.

The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (

) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (

;

) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (

) and PAGM (

) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Alpha-D-phosphohexomutase, alpha/beta/alpha domain III (A-D-PHexomutase_a/b/a-III)
Type: Domain

This entry represents domain III found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer α/β/α topology.

The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (

) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (

;

) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (

) and PAGM (

) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Urease, alpha subunit (Urease_asu)
Type: Family

Urease (urea amidohydrolase,

) is a nickel-binding enzyme that catalyses the hydrolysis of urea to form ammonia and carbamate . It is mainly found in plant seeds, microorganisms and invertebrates. In plants, urease is a hexamer of identical chains, but the subunit composition of urease from different sources varies , in bacteria it consists of either two or three different subunits (alpha, beta and gamma).

Urease binds two nickel ions per subunit; four histidine, an aspartate and a carbamated-lysine serve as ligands to these metals; an additional histidine is involved in the catalytic mechanism . The urease domain forms an (alpha β)(8) barrel structure with structural similarity to other metal-dependent hydrolases, such as adenosine and AMP deaminase and phosphotriesterase. Urease is unique among nickel metalloenzymes in that it catalyses a hydrolysis rather than a redox reaction.

The orthologous protein is known as the alpha subunit (ureC) in most other bacteria.In Helicobacter pylori, the gamma and beta domains are fused and called the alpha subunit (

). The catalytic subunit (called beta or B) has the same organisation as the Klebsiella alpha subunit. Jack bean (Canavalia ensiformis) urease has a fused gamma-beta-alpha organisation (

). This entry describes the urease alpha subunit UreC (designated beta or B chain, UreB in Helicobacter species).
Galactose-1-phosphate uridyl transferase, N-terminal (GalP_Utransf_N)
Type: Domain

Galactose-1-phosphate uridyl transferase catalyses the conversion of UDP-glucose and alpha-D-galactose 1-phosphate to alpha-D-glucose 1-phosphate and UDP-galactose during galactose metabolism. The enzyme is present in prokaryotes and eukaryotes. Defects in GalT in humans is the cause of galactosemia, an inherited disorder of galactose metabolism that leads to jaundice, cataracts and mental retardation.

This domain describes the C-terminal of Galactose-1-phosphate uridyl transferase. SCOP reports fold duplication of the C-terminal with the N-terminal domain. Both are involved in Zn and Fe binding.
Galactose-1-phosphate uridyl transferase, C-terminal (GalP_Utransf_C)
Type: Domain

Galactose-1-phosphate uridyl transferase catalyses the conversion of UDP-glucose and alpha-D-galactose 1-phosphate to alpha-D-glucose 1-phosphate and UDP-galactose during galactose metabolism. The enzyme is present in prokaryotes and eukaryotes. Defects in GalT in humans is the cause of galactosemia, an inherited disorder of galactose metabolism that leads to jaundice, cataracts and mental retardation.

This domain describes the C-terminal of Galactose-1-phosphate uridyl transferase. SCOP reports fold duplication of the C-terminal with the N-terminal domain. Both are involved in Zn and Fe binding.
Phosphoglucomutase, alpha-D-glucose specific (PGM_a-D-Glc-sp)
Type: Family

Phosphoglucomutase, alpha-D-glucose phosphate-specific (

) links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose .

The alpha-D-phosphohexomutases include several related enzymes that catalyse a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model .
Omega-agatoxin type II/III, conserved site (Omega-agatoxin_II/III_CS)
Type: Conserved_site

Spider venoms often contain many active peptides, such as neurotoxins, lectins, and enzyme inhibitors, which are important for both hunting and defence. Starting from a common ancestor these peptides have evolved into a diverse array of toxins with different structures and functions. These toxins contain contain a relatively high number of cysteine residues, generally ranging from 6 to 14 . Several peptide toxins, collectively referred to as omega-toxins, block the different types of voltage-gated Ca2+ channels with differential selectivity.
Amidophosphoribosyltransferase (PurF)
Type: Family

This family contains sequences which are members of the MEROPS peptidase family C44 (glutamine phosphoribosylpyrophosphate amidotransferase precursor, clan PB(C)) and sequences which are classed as non-peptidase homologues. These are sequences either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.

Purine nucleotides are synthesised both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. Amidophosphoribosyltransferase (

) is the rate-limiting enzyme in the de novo pathway of purine ribonucleotide synthesis and is regulated by feedback inhibition by AMP and GMP .

5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H2O

This enzyme crystallises as a homotetramer, but can also exist as a homodimer .
Glucosamine-fructose-6-phosphate aminotransferase, isomerising (GFAT)
Type: Family

Glucosamine:fructose-6-phosphate aminotransferase (GFAT or GlmS,

) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars .

This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologues.
Cysteine synthase (Cys_synth)
Type: Family

Cysteine synthase (also known as O-acetylserine (thiol)-lyase or O-acetyl-L-serine sulfhydrylase) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM) . CysM differs from CysK in that it can also use thiosulphate instead of sulphide, to produce cysteine.
Cystathionine beta-synthase (Cysta_beta_synth)
Type: Family

Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. Cysteine synthase (O-acetylserine (thiol)-lyase) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid -the function of many of these enzymes is unproven.

This entry includes human CBS protein, which is a hydro-lyase catalysing the first step of the transsulfuration pathway, where the hydroxyl group of L-serine is displaced by L-homocysteine in a beta-replacement reaction to form L-cystathionine, the precursor of L-cysteine. This catabolic route allows the elimination of L-methionine and the toxic metabolite L-homocysteine . Mutations in the CBS gene cause cystathionine beta-synthase deficiency (CBSD), an enzymatic deficiency resulting in altered sulfur metabolism and homocystinuria .
Cysteine synthase CysM (CysM)
Type: Family

Cysteine synthase (O-acetylserine (thiol)-lyase,

) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM). CysM differs from CysK (

) in that it can also use thiosulphate instead of sulphide, to produce cysteine thiosulphonate instead of cysteine.
Cysteine synthase CysK (CysK)
Type: Family

Cysteine synthase (O-acetylserine (thiol)-lyase,

) is the enzyme responsible for the formation of cysteine from O-acetyl-serine and hydrogen sulphide with the concomitant release of acetic acid. In bacteria such two forms of the enzyme are known (genes cysK and cysM). CysK differs from CysM in that it can also use sulphide instead of thiosulphate, to produce cysteine instead of cysteine thiosulphonate.

This entry represents CysK-type cysteine synthases. It includes beta-cyanoalanine synthase, a mitochondrial cysteine synthase-like protein from plants .
L-threonine-O-3-phosphate decarboxylase (CobD)
Type: Family

L-threonine-O-3-phosphate decarboxylase (CobD) was shown to decarboxylate L-threonine O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, which is the precursor for the linkage between the nucleotide loop and the corrin ring in the biosynthesis of cobalamin . The molecule is a dimer where each subunit consists of a large and small domain . This family contains pyridoxal phosphate-binding class II aminotransferases closely related to histidinol-phosphate aminotransferase (HisC).
Histidinol-phosphate aminotransferase family (HisP_aminotrans)
Type: Family

The histidinol phosphate aminotransferase family consists of class I pyridoxal-5'-phosphate (PLP)-dependent enzymes that catalyze a step of L-histidine biosynthesis . These proteins are highly specific enzymes in the sense that no other aminotransferases are known to be capable of utilizing imidazoleacetol phosphate, with deletions leading to auxotrophy. A subgroup of these enzymes have broader substrate specificity and are capable of using aromatic amino acid substrates in vitro and in vivo
Formate-dependent phosphoribosylglycinamide formyltransferase (PurT)
Type: Family

The formation of isocyanate, a precursor of adenylate and guanylate, from 5-phosphoribosyl 1-pyrophosphate in the de novo purine biosynthesis pathway is basically composed of 10 steps of reactions . Formate-dependent phosphoribosylglycinamide formyltransferase (PurT, also known as phosphoribosylglycinamide formyltransferase 2) belongs to the ATP-grasp superfamily of enzymes and catalyses the third step in the de novo purine biosynthesis pathway, the formylation of glycinamide ribonucleotide that requires Mg2, ATP and formate .
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (UDP-N-AcMur_synth)
Type: Family

The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:

(1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).

(2) addition of a short polypeptide chain to the UDPMurNAc.

(3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.

Stage two involves four key Mur ligase enzymes: MurC (

) , MurD (

) , MurE (

) and MurF (

) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid . All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that binds the incoming amino acid . Residues found in the three domains (the Asp50, Lys130 (GKT motif), and Glu174 residues, MurC numbering) are involved in the catalytic process . The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .

This entry represents UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (also known as UDP-MurNAc-pentapeptide synthetase, MurF,

), which is required to catalyze the final step in the synthesis of the cytoplasmic precursor of the bacterial cell wall peptidoglycan.
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine.
. The crystal structure of the MurF apo-enzyme has been determined and refined to 2.3 A resolution. It contains three consecutive open α/β-sheet domains. The topology of the N-terminal domain of MurF is unique, while its central and C-terminal domains exhibit similar mononucleotide and dinucleotide-binding folds to MurD. The apo-enzyme of MurF crystal structure reveals an open conformation with the three domains juxtaposed in a crescent-like arrangement creating a wide-open space where substrates are expected to bind. As such, catalysis is not feasible and significant domain closure is expected upon substrate binding .
ATP synthase, F0 complex, subunit b, bacterial (ATP_synth_F0_bsu_bac)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This entry represents subunit b from the F0 complex in F-ATPases found in bacterial plasma membranes. The b subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit b .
Tetrahydromethanopterin S-methyltransferase, subunit C (THM_MeTrfase_su_C)
Type: Family

This entry represents the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit C in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Tetrahydromethanopterin S-methyltransferase, subunit G (THM_MeTrfase_su_G)
Type: Family

This entry represents the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Photosystem II protein D1 (PSII_D1)
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 D1 protein (also known as PsbA), which forms the reaction core of PSII as a heterodimer with the D2 protein. In higher plants, the N-terminal residues of both proteins, which are exposed to the stromal surface, can be reversibly phosphorylated. After insertion in the membrane, the C-terminal of the D1 protein is cleaved by a C-terminal processing protease to yield the mature protein . This processing is essential for the assembly of a functional 4-atom manganese cluster, which involves binding to a highly conserved C-terminal alanine 344 . The Mn cluster is located on the lumenal surface of the D1 and D2 proteins . In addition to the Mn cluster, the D1/D2 core binds to a number of cofactors, including: two pheophytin molecules, only one of which is phytochemically active; non-haem iron; and two quinones, Qa (bound to D2) and Qb (bound to D1). Upon light excitation, an electron is transferred from the primary donor (chlorophyll a) via intermediate acceptor pheophytin to the primary quinone Qa, then to the secondary quinone Qb. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose.