SII-SWORD/CoKE huggingface dataset:
Urocanase-like (Urocanase-like)
Type: Family

Urocanase (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyses the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate:

urocanate + H
2
O = 4,5-dihydro-4-oxo-5-imidazolepropanoate

Urocanase is found in some bacteria (gene hutU) , in the liver of many vertebrates, and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD
+
and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD
+
.

This enzyme is a symmetric homodimer with tightly bound NAD+ cofactors. Each subunit consists of a typical NAD-binding domain inserted into a larger core domain that forms the dimer interface .

This entry also includes S-methyl thiourocanate hydratase which doesn't use urocanate as a substrate but rather catalyses the 1,4-addition of H2O to S-methyl thiourocanate, leading to the formation of S-methyl-thiohydantoin-5-propanoate, the second step in S-methyl ergothioneine degradation .
Large ribosomal subunit protein eL19, conserved site (Ribosomal_eL19_CS)
Type: Conserved_site

This entry represents a conserved site in the ribosomal protein eL19 from eukaryotes and archaea ; it is part of the large ribosomal subunit.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
DNA primase small subunit PriS (DNA_primase_ssu_PriS)
Type: Family

DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits .

This family represents sequences of the DNA primase small subunit PriS from archaea.
DNA primase large subunit PriL (DNA_primase_lsu_PriL)
Type: Family

This family consists of DNA primase large subunit PriL from archaea.

DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS or Pri1) and a large subunit (PriL or Pri2). In the yeast Saccharomyces cerevisiae the small subunit is 48kDa and the large subunit 58kDa . In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity and the the ATP binding site reside within PriS , the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of the products to DNA polymerase alpha . Primase function has also been demonstrated for human and mouse primase subunits .
3-phenylpropionate-dihydrodiol/cinnamic acid-dihydrodiol dehydrogenase HcaB (Dihydrodiol_DH_HcaB)
Type: Family

The HcaB protein is a dehydrogenase which converts 3-phenylpropionate-dihydrodiol and cinnamic acid-dihydrodiol into 3-(2,3-dihydroxylphenyl)propanoic acid and 2,3-dihydroxicinnamic acid, respectively . This protein functions in the dioxygenolytic pathway for catabolism of phenylpropanoid compounds such as cinnamic acid and 3-phenylpropionic acid .
Nitrous-oxide reductase (NO_Rdtase)
Type: Family

Nitrous-oxide reductase is part of a bacterial respiratory system which is activated under anaerobic conditions in the presence of nitrate or nitrous oxide. NosZ, one of the members of this family, is the nitrous-oxide reductase structural protein, with an N-terminal twin-arginine translocation (TAT) signal sequence. The TAT system replaces the Sec system for export of proteins with bound cofactor .
D-aminopeptidase (DAP)
Type: Family

This entry represents D-aminopeptidase that hydrolyses N-terminal residues in D-amino acid-containing peptides (

).

D-aminopeptidase is a dimeric enzyme with each monomer being composed of three domains; domain B is connected to domain A, the catalytic domain, by an eight-residue sequence, and also interacts with both domains A and C via non-covalent bonds. Domain B probably functions in maintaining domain C in a good position to interact with the catalytic domain .
Primosomal replication protein PriB (Prisomal_replication_PriB)
Type: Family

PriB, also known as Primosomal replication protein N, is a component of the preprimosomal complex. The preprimosomal complex is composed of one monomer of PriC and DnaT, two monomers of PriA, two dimers of PriB and one hexamer of DnaB. Upon transient interaction with DnaG it forms the primosome .

PriB binds single-stranded DNA at the primosome assembly site (PAS) . Assembly of the primosome is initiated by interactions of PriA and PriB with ssDNA and the PAS .
Deoxyribose-phosphate aldolase type II (DeoC_typeII)
Type: Family

Deoxyribose-phosphate aldolase is a widely distributed enzyme, which catalyses the following reversible reaction:

2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde

While the physiological role of this enzyme remains unknown in eukaryotes, in prokaroytes it is thought to function in the catabolism of deoxyribonucleotides .

In all studied structures, the deoxyribose-phophate aldolase subunits adopt the classical eight-bladed TIM barrel fold . The oligomerisation state of the enzyme appears to depend on the living temperature of the organism - the Escherichia coli enzyme (

) is a homodimer, while the enzymes from the thermophilic microorganisms Thermus thermophilus and Aeropyrum pernix (

) are homotetramers. The degree of oligomerisation does not, however, appear to affect catalysis.

This entry represents deoxyribose-phosphate aldolase from Proteobacteria.
Beta-lactamase, class-A active site (Beta-lactam_class-A_AS)
Type: Active_site

This entry represents a short region that contains the active site serine residue in the class A beta-lactamases that belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE).

Beta-lactamase catalyses the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins. There are four groups, classed A, B, C and D according to sequence, substrate specificity, and kinetic behaviour. Class A (penicillinase-type) is the most common . The genes for class A beta-lactamases are widely distributed in bacteria, frequently located on transmissible plasmids in Gram-negative organisms, although an equivalent chromosomal gene has been found in a few species . Class A, C and D beta-lactamases are serine-utilising hydrolases, while class B enzymes utilise a catalytic zinc centre instead. The 3 classes of serine beta-lactamase are evolutionarily related and belong to a superfamily that also includes DD-peptidases and other penicillin-binding proteins . All these proteins contain an S-x-x-K motif, the Ser being the active site residue. Although clearly related, however, the sequences of the 3 classes of serine beta-lactamases vary considerably outside the active site.

This entry represents the Group 2 beta-lactamases, which correspond to the penicillinases and cephalosporinases, which are inhibited by clavulanic acid. They corresponding to the molecular classes A and D reflecting the original TEM and SHV genes. However, because of the increasing number of TEM and SHV derived beta-lactamases, they have been divided into two subclasses, 2a and 2b:

The 2a subgroup contains just penicillinases.

The 2b subgroup contains broad spectrum beta-lactamases, meaning that they are capable of inactivating penicillins and cephalosporins at the same rate. Furthermore, new subgroups were segregated from subgroup 2b based on their activity against certain antibiotics and resistance to clavulanic acid.

Molecular Class D or A Subgroup 2d enzymes inactivate cloxacillin more than benzylpenicillin, with some activity against carbenicillin; these enzymes are poorly inhibited by clavulanic acid, and some of them are extended spectrum beta-lactamases (ESBLs).
Large ribosomal subunit protein eL14, archaeal (Ribosomal_eL14_arc)
Type: Family

This entry represents archaebacterial ribosomal protein eL14.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Sirohydrochlorin cobaltochelatase (SiroHydchlorin_Cochelatase)
Type: Family

This entry represents archaeal sirohydrochlorin cobaltochelatase. This enzyme chelates cobalt to the cobalamin precursor as part of the anaerobic pathway to cobalamin biosynthesis .
Acetoacetate decarboxylase, bacterial (Acetoacetate_decarboxylase_bac)
Type: Family

This entry represents bacterial acetoacetate decarboxylases.

Acetoacetate decarboxylase (ADC) is involved in solventogenesis in certain bacteria, which occurs at the end of the exponential growth phase when there is a metabolic switch from classical sugar fermentation with the production of acetate and butyrate to the re-internalisation and oxidation of these acids to acetate and butanol . In Clostridium, SpoOA controls the switch from acid to solvent production. A SpoAO-binding motif occurs in the gene encoding ADC .
Large ribosomal subunit protein eL32, archaeal (Ribosomal_eL32_arc)
Type: Family

This entry represents the archaeal 50S eL32 ribosomal proteins.

eL32 is a protein from the large ribosomal subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. eL32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. eL32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, eL32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Cytochrome c6 (Cyt_C6)
Type: Family

Cytochrome c (CytC) proteins can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes.

Ambler recognised four classes of cytC.

Class I includes the low-spin soluble CytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I CytC were further subdivided into five classes, IA to IE. Class IC, 'split-alpha-band' Cyt C, possess a widened or split alpha-band of lowered absorptivity. This class includes dihaem Cyt C4 and monohaem Cyt C6 (Cyt C-553) and Cyt C-554.

The 3D structures of Chlamydomonas reinhardtii Cyt C6 and Desulfovibrio vulgaris Cyt C-553 have been determined. The proteins consist of 4 α-helices; three 'core' helices form a 'basket' around the haem group, with one haem edge exposed to the solvent.

This entry also includes Cytochrome c6 from Arabidopsis, which functions as an electron carrier between membrane-bound cytochrome b6-f and photosystem I in oxygenic photosynthesis .
IMP biosynthesis enzyme PurP (IMP_biosynth_PurP)
Type: Family

The last two steps of
de novo
purine biosynthesis are:

i) conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR)

ii) conversion of FAICAR to inosine5'-monophopsphate (IMP)

In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH . Archaea do not appear to posses PurH, however, and perform these reactions by a different mechanism . In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species .

This entry represents the 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase also known as PurP.
Large ribosomal subunit protein eL40, archaeal (Ribosomal_eL40_arc)
Type: Family

This family represents the archaeal eL40 ribosomal protein .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
15,16-dihydrobiliverdin:ferredoxin oxidoreductase (DiHydbiliverdin_OxRdtase)
Type: Family

This enzyme catalyzes the two-electron reduction of biliverdin IX-alpha at the C15 methine bridge .
Coenzyme F420:L-glutamate ligase, archaeal (F420_ligase_CofE_arc)
Type: Family

This entry contains coenzyme F420:L-glutamate ligase (also known as F420-0:gamma-glutamyl ligase) from archaea. It catalyses the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives .
Protein arginine kinase (Arg_Kinase)
Type: Family

This family of bacterial arginine kinases catalyse the transfer of phosphate from ATP to arginine. Protein arginine phosphorylation is involved in the regulation of many critical cellular processes, such as protein degradation, competence and stress responses . Bacterial protein arginine kinase McsB main targets comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine . McsB has been shown to phosphorylate and inhibit global heat shock repressor CtsR . Furthermore, McsB is an adaptor for the ClpCP protease. McsB is activated during heat stress by autophosphorylation, allowing the controlled degradation of CtsR by ClpCP . It is also required for de-localization of competence proteins .
Bifunctional F420 biosynthesis protein FbiB (FbiB)
Type: Family

FbiB catalyses the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives . It is also involved in the FMNH2-dependent reduction of dehydro-F420-0 to form F420-0 .

This entry represents the bacterial form of the enzyme.