SII-SWORD/CoKE huggingface dataset:
Ferredoxin-like, FixX (Fd_FixX)
Type: Family

Rhizobium meliloti (Sinorhizobium meliloti) FixX protein contains a cluster of cysteine residues characteristic of bacterial ferredoxins . The gene product from Escherichia coli could be a 3Fe-4S cluster-containing protein. These are highly homologous to an Azotobacter ferredoxin which has been shown to donate electrons to nitrogenase .
Cytochrome c, Bacillus subtilis c550-type (Cyt_c_BACSU-c550-type)
Type: Family

These Class I cytochromes from Gram-positive bacteria are membrane anchored via a lipid anchor in the N-terminal region. Properties of the Bacillus subtilis protein are described in .
Glutamate synthase, eukaryotic (Glu_synth_euk)
Type: Family

This group represents the eukaryotic type of glutamate synthase (NADH-GOGAT,

). This pyridine-linked form is found in both photosynthetic and nonphotosynthetic eukaryotes. It displays a single-subunit structure corresponding to the fusion of the small and the large bacterial subunits.

Glutamate synthase (GOGAT, GltS) is a complex iron-sulphur flavoprotein that catalyses the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the bacterial, yeast and plant pathways for ammonia assimilation . GOGAT is a multifunctional enzyme that functions through three distinct active centres carrying out multiple reaction steps: L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor . The small subunit functions as a FAD-dependent NADPH oxidoreductase, which serves to transfer reducing equivalents to the site of glutamate synthesis on the large subunit through the enzyme [3Fe-4S] cluster (on the large subunit) and at least one of its [4Fe-4S] centres . The large subunit contains the GltS L-glutamine amidotransferase (GAT) site where L-Gln binds and is hydrolysed to yield L-Glu and ammonia. The latter is transferred through the intramolecular ammonia tunnel to the glutamate synthase site where 2-OG binds, is converted to the iminoglutarate (2-IG) intermediate, and reduced to L-Glu by receiving reducing equivalents from the reduced FMN cofactor at this site .

There are four classes of GOGAT :

1. Bacterial NADPH-dependent GOGAT (NADPH-GOGAT,

). This standard bacterial NADPH-GOGAT is composed of a large (alpha, GltB) subunit and a small (beta, GltD) subunit.

2. Ferredoxin-dependent form in cyanobacteria and plants (Fd-GOGAT from photosynthetic cells,

) displays a single-subunit structure corresponding to the large bacterial subunit.

3. Pyridine-linked form in both photosynthetic and nonphotosynthetic eukaryotes (eukaryotic GOGAT or NADH-GOGAT,

) displays a single-subunit structure corresponding to the fusion of the small and the large bacterial subunits.

4. The archaeal type with stand-alone proteins corresponding to the N-terminal, FMN-binding, and the C-terminal domains of the large subunit (

,

), and to the small subunit.

The large subunit of GOGAT consists of three domains: N-terminal domain (amidotransferase domain

); central (consisting of

and the FMN-binding domain

), and the C-terminal domain (

).

The N-terminal amidotransferase domain is characterised by a four layer α/β/β/α architecture and is similar to other Ntn-amidotransferases . It contains the typical catalytic centre of Ntn-amidotransferases, and the N-terminal Cys-1 catalyses the hydrolysis of L-glutamine generating ammonia and the first molecule of L-glutamate .
Peptidase S1A, coagulation factor VII/IX/X/C/Z (Pept_S1A_FX)
Type: Family

This group of plasma glycoproteins includes coagulation factors VII, IX, and X, and proteins C and Z, which belong to MEROPS peptidase family S1, subfamily S1A (chymotrypsin, clan PA(S)). All but protein Z are peptidases and are involved in blood coagulation. The precursors contain a signal sequence, propeptide, Gla domain, two EGF domains (although sometimes only one is detected by Pfam), and a trypsin domain. Except for protein Z, they are further cleaved between the second EGF domain and the trypsin domain into light and heavy chains, which are connected by a disulphide bond. Glutamic acid residues in the Gla domain undergo vitamin K-dependent carboxylation, allowing this region to bind calcium and membrane phospholipid . The propeptide region is important in providing a recognition site for the gamma-carboxylase . Typically one aspartic acid residue in the light chain is post-translationally modified to erythro-beta-hydroxyaspartic acid .
Diguanylate cyclase/phosphodiesterase (Diguanyl_cyclase/Pdiesterase)
Type: Family

Members of this group are signal transduction proteins that are direct oxygen sensors and are involved in regulation of cellular processes via the effector molecule cyclic diguanylate (c-di-GMP, bis(3',5')-cyclic diguanylic acid). They contain PAS/PAC, GGDEF, and EAL domains and have diguanylate cyclase and phosphodiesterase activities. Related groups with similar domain architectures contain different versions of PAS/PAC domain, and are thought to have different, often not yet determined biological functions.

Escherichia coli Dos (YddU or DosP) and Komagataeibacter xylinus (Gluconacetobacter xylinus or Acetobacter xylinum) PdeA1 proteins have been shown to be direct, haem-based oxygen sensors . Their N-terminal PAS domains are responsible for haem-binding . PAS/PAC is a ubiquitous intracellular sensory domain. It is located in the cytoplasm and sense changes in redox potential in the electron transport system or overall cellular redox status. PAS domains can monitor changes in light, oxygen or small ligands in a cell, and sense environmental factors that cross the cell membrane and/or affect cell metabolism . In the haem-containing subgroup of PAS domains, the haem pocket acts as a ligand-specific trap . The ligand binding to a haem-containing PAS domain leads to either activation or inhibition of a regulated (catalytic) domain (here, GGDEF and/or EAL domains). Phosphodiesterase activity with cAMP of E. coli Dos has been shown to be regulated by the haem redox state . Similarly, Komagataeibacter xylinus PdeA1 is regulated by reversible binding of O
2
to the haem .

The catalytic function of the members of this group has also been experimentally determined.

Cyclic di-GMP (c-di-GMP) is the specific nucleotide regulator of beta-1,4-glucan (cellulose) synthase in Komagataeibacter xylinus . In a study of the regulation of biosynthesis of extracellular cellulose in Komagataeibacter xylinus , the search for the enzymes that synthesise and hydrolyse cyclic di-GMP resulted in the identification of six proteins with identical domain architecture containing PAS, GGDEF and EAL domains. Three of them exhibited diguanylate cyclase activity (Dgc1-3), and three others - phosphodiesterase activity (PdeA1-3) . Likewise, E. coli Dos has been shown to have phosphodiesterase activity .

Genetic complementation using genes from three different bacteria encoding proteins with GGDEF domains as the only element in common indicate that the GGDEF domain is responsible for the diguanylate cyclase activity of these proteins . Even prior to these results, the notion that the GGDEF domain is a diguanylate cyclase was supported by the detailed analysis of its sequence, which shows conservation of the proposed nucleotide-binding loop in alignment with eukaryotic adenylate cyclases .

By exclusion, the EAL domain emerged as the best candidate for the role of c-di-GMP phosphodiesterase. Indeed, the sequence of this domain contains several conserved aspartates, which could participate in metal binding and form a phosphodiesterase active site .
Protein kinase C (PKC)
Type: Family

This group represents protein kinase C (PKC), including zeta/iota types from mammals, protein kinase C-like 3 from round worms and atypical protein kinase C (aPKC) from fruit flies .
Tyrosine-protein kinase, non-receptor SYK/ZAP-70 (Tyr_kinase_non-rcpt_SYK/ZAP70)
Type: Family

Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity :

Serine/threonine-protein kinases

Tyrosine-protein kinases

Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)

Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .

Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups :

Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis . RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction .

Cytoplasmic/non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases .

This entry represents the non-receptor tyrosine kinases SYK and ZAP-70 :

SYK is a positive effector of BCR-stimulated responses. It couples the B-cell antigen receptor (BCR) to the mobilisation of calcium ion, either through a phosphoinositide 3-kinase-dependent pathway (when not phosphorylated on tyrosines of the linker region), or through a phospholipase C-gamma-dependent pathway (when phosphorylated on Tyr-342 and Tyr-346). Therefore, the differential phosphorylation of Syk can determine the pathway by which BCR is coupled to the regulation of intracellular calcium ion .

ZAP70 plays a role in T-cell development and lymphocyte activation. It is essential for TCR-mediated IL-2 production. Isoform 1 of ZAP70 induces TCR-mediated signal transduction, isoform 2 does not .
3-isopropylmalate dehydratase, fused small/large subunit (3-IsopropMal_deHydtase_ssu/lsu)
Type: Family

3-isopropylmalate dehydratase (or isopropylmalate isomerase;

) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase

, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast .

This group represents 3-isopropylmalate dehydratase: with fused small and large subunits .
Molybdenum cofactor biosynthesis protein MoaB (MoaB)
Type: Family

This entry represents the MoaB family of predicted molybdenum cofactor biosynthesis proteins and related sequences .
Bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA (MoaC_MogA)
Type: Family

This entry includes a group of molybdenum cofactor biosynthesis bifunctional proteins. The proteins are composed of 2 domains: a molybdenum cofactor biosynthesis protein C-like domain and a molybdenum cofactor biosynthesis protein B-like domain. Together with MoaA, they are involved in the conversion of 5'-GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z).
N-acetylglucosamine-6-sulfatase (GlcNAc_6-SO4ase)
Type: Family

N-acetylglucosamine-6-sulfatase catalyses the hydrolysis of the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of heparan sulfate and keratan sulfate . This enzyme is deficient in Sanfilippo Syndrome type IIID . Mucopolysaccharidosis type III (MPS-III), or Sanfilippo syndrome, is a group of lysosomal storage disorders caused by impaired degradation of heparan sulfate.
Electron transfer flavoprotein, beta subunit (ETF_b)
Type: Family

Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) .
D-lactate dehydrogenase (D_lactate_DH)
Type: Family

D-lactate dehydrogenases catalyse the reversible oxidation of D-lactate to pyruvate. This entry represents the NADH-independent D-lactate dehydrogenases found in many bacterial species. These are membrane-associated respiratory enzymes which contain an FAD cofactor and transfer electrons derived from susbstrate oxidation to the electron transfer chain. The energy derived from this reaction can be coupled either to ATP generation or the active uptake of solutes. The Escherichia coli enzyme (

) is a peripheral membrane enzyme located on the cyctoplasmic side of the inner membrane, which passes the electrons derived from substrate oxidation to the quinone component of the electron transfer chain . It is composed of three domains: an FAD-binding domain, a cap domain and a membrane-binding domain. The FAD-binding domain has a similar fold to that of other FAD-linked enzymes, being composed of two α-β subdomains, with the FAD cofactor being accommodated between them. The cap domain forms an α-β-α sandwich, while the membrane-binding region is composed of four α helices which show an excess of basic residues over acidic ones. The enzyme is thought to be anchored to the membrane by electrostatic interactions between these basic reidues and the negatively charged phospholipid head groups of the membrane. The active site of the enzyme is not known, but is thought to be located close to the FAD-binding site, at the interface of all three domains.

Proteins in this entry also include quinone-dependent D-lactate dehydrogenase Dld from Corynebacterium glutamicum. It is essential for growth with D-lactate as sole carbon source .
Glycolate oxidase, iron-sulphur subunit (Glc_ox_4Fe-4S)
Type: Family

This group represents a glycolate oxidase, iron-sulphur subunit .
Acyl-CoA oxidase (Acyl-CoA_oxidase)
Type: Family

Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids and a major producer of hydrogen peroxide (H2O2) .

Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain . Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments .
Dihydrofolate reductase (DHFR)
Type: Family

Dihydrofolate reductase (DHFR) (

) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in
de novo
synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) , and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood .

Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar . The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself .
Bifunctional dihydrofolate reductase/thymidylate synthase (DHFR-TS)
Type: Family

This group represents a bifunctional dihydrofolate reductase/thymidylate synthase found in some plant species and protozoal parasites including malarial species and trypanosomes. In other species dihydrofolate reductase and thymidilate synthase are encoded on separate polypeptides.

Thymidylate synthase (

) catalyses the reductive methylation of dUMP to dTMP with concomitant conversion of 5,10-methylenetetrahydrofolate to dihydrofolate:

5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP

This provides the sole
de novo
pathway for production of dTMP and is the only enzyme in folate metabolism in which the 5,10-methylenetetrahydrofolate is oxidised during one-carbon transfer . The enzyme is important for regulating the balanced supply of the 4 DNA precursors in normal DNA replication: defects in the enzyme activity affecting the regulation process can cause various biological and genetic abnormalities. A cysteine residue is involved in the catalytic mechanism (it covalently binds the 5,6-dihydro-dUMP intermediate). The sequence around the active site of this enzyme is conserved from phages to vertebrates.

Dihydrofolate reductase (DHFR) (

) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate:

5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+

This is an essential step in
de novo
synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) , and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate.
Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood .

As this enzyme is essential in both nucleic acid and amino acid biosynthesis, it is an important target of antiparasitic drugs. Resistance to antimalarial drugs that target this enzyme is often due to mutations that prevent drug binding but maintain enzyme activity. The structure of the wild-type and drug resistant malarial enzymes provides insights into the development of resistance and suggests approaches for the design of new drugs against this target .
Adenine modification methylase, M.EcoRV-type (M_m6A_EcoRV)
Type: Family

In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. There are 2 major classes of DNA methyltransferase that differ in the nature of the modifications they effect. The members of one class (C-MTases) methylate a ring carbon and form C5-methylcytosine (see

). Members of the second class (N-MTases) methylate exocyclic nitrogens and form either N4-methylcytosine (N4-MTases) or N6-methyladenine (N6-MTases). Both classes of MTase utilise the cofactor S-adenosyl-L-methionine (SAM) as the methyl donor and are active as monomeric enzymes .

N-6 adenine-specific DNA methylases (

) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. They include enzymes are found in bacterial restriction-modification systems, as well as solitary enzymes that do not have a restriction enzyme counterpart .

Proteins in this entry are homologous to Dam methyltransferase (

) from Escherichia coli which recognises the sequence GATC and methylates the adenine moeity. This protein is not part of a restriction modification system and its activity influences cellular functions such as gene transcription, DNA mismatch repair, initiation of chromosome replication and nucleoid structure . It is dispensible in E. coli, but has been shown to be required for viability in Yersinia and Vibrio species, virulence in Salmonella, and replication in some bacteriophages. Dam methyltransferase consists of a seven-stranded β sheet sandwiched between two layers of α helices . The β sheet contains the catalytic domain, while the target recognition domain is composed of five α helices and a β hairpin. The methyl donor binds to a region of the β sheet, surrounded by conserved residues, which is next to a narrow surface pocket thought to contain the active site.