SII-SWORD/CoKE huggingface dataset:
Photosystem II PsbX, type 2 subfamily (PSII_PsbX_type_2_subfam)
Type: Family

The protein family of PsbX, also known as Photosystem II reaction center protein X, can be divided into two subfamilies; this one, which is found only in some Prochlorococcus, and a shorter one with a wider taxonomic distribution. This entry represents type 1 subfamily, whose members are currently uncharacterised.

The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII , and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) 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 .
Peptidase HybD-like domain superfamily (Pept_HybD-like_dom_sf)
Type: Homologous_superfamily

This superfamily represents a structural domain described for HybD and related proteins such as the germination protease from Gram-positive bacteria. It consists of a twisted five-stranded β-sheet surrounded by four and three helices, respectively, on each side .
Photosystem II PsbX, type 1 subfamily (PSII_PsbX_type_1_subfam)
Type: Family

The protein family of PsbX, also known as Photosystem II reaction center protein X, can be divided into two subfamilies; this one and a longer one found in most but not all Prochlorococcus. This entry represents type 1 subfamily, whose members are mainly found in cyanobacteria, red algae and diatoms, including members from Synechocystis and Thermosynechococcus elongatus .

The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII , and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) 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 .
Acetyl-CoA decarbonylase/synthase complex subunit beta, archaeal (CO_DH/Ac-CoA_synth_bsu_arc)
Type: Family

The carbon monoxide dehydrogenase alpha subunit (

) catalyses the interconversion of CO and CO2 and the synthesis of acteyl-coA from the methylated corrinoid/iron sulphur protein, CO and CoA.

The ACDS complex is made up of alpha, epsilon, beta, gamma and delta chains with a probable stoichiometry of (alpha(2)epsilon (2))(4)-beta(8)-(gamma(1)delta(1)).

This entry represents part of the complex that catalyses the reversible cleavage of acetyl-CoA, allowing growth on acetate as sole source of carbon and energy in archaea.

Acetyl-CoA + [acetyl-CoAdecarbonylase/synthase complex beta subunit] = CoA + acetyl-[acetyl-CoA decarbonylase/synthase complex beta subunit].
Argininosuccinate synthase, type 1 subfamily (Arginosuc_synth_type_1_subfam)
Type: Family

This entry represents argininosuccinate synthase, type 1 subfamily.

Argininosuccinate synthase (

) (AS) is a urea cycle enzyme that catalyses the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate .

In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation.

AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.
D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit KbaZ (TagBP_ald_KbaZ)
Type: Family

Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases . However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity . It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ and other members of this family have been debated .

This entry represents the KbaZ proteins.
D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit GatZ (TagBP_ald_GatZ)
Type: Family

Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases . However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity . It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ and other members of this family have been debated .

This entry represents the GatZ proteins.
Argininosuccinate synthase, type 2 subfamily (Arg_succ_synth_type2_subfam)
Type: Family

Argininosuccinate synthase (

) (AS) is a urea cycle enzyme that catalyses the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate .

In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation.

AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.

This entry represents argininosuccinate synthase, type 2 subfamily.
Malonate decarboxylase/citrate lyase acyl carrier protein (Mal_deCO2ase/Cit_lyase_ACP)
Type: Family

This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Large ribosomal subunit protein eL24, conserved site (Ribosomal_eL24_CS)
Type: Conserved_site

This entry represents a conserved sequence region found towards the N terminus of ribosomal protein eL24 (previously known as L24). It is also found in ribosomal protein eL24-like, an essential protein with similarity to Rpl24Ap and Rpl24Bp, which is associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis .

A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian ribosomal protein eL24; yeast ribosomal protein eL24A/B;
Kluyveromyces lactis
ribosomal protein eL24;
Arabidopsis thaliana
ribosomal protein eL24y/z;
Haloarcula marismortui
ribosomal protein eL24; and
Methanocaldococcus jannaschii
protein eL24. These proteins have 60 to 160 amino-acid residues.

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 .
L-rhamnonate dehydratase (L-Rhamnon_dehydrat)
Type: Family

L-rhamnonate dehydratase belongs to the mandelate racemase/muconate lactonizing enzyme family, specifically the RhamD subfamily. L-rhamnonate dehydratase (

) catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR)

L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate+ H(2)O.

This reaction proceeds via a syn dehydration.
Arginine exporter protein ArgO, enterobacteria (Arg_export_ArgO_enterobac)
Type: Family

The arginine exporter protein ArgO is involved in the export of arginine and is important to control the intracellular level of arginine and the correct balance between arginine and lysine .
Carnitine operon protein CaiE (CaiE)
Type: Family

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.

The function of the CaiE protein is not known, but overexpression has been shown to stimulate the activity of CaiB and CaiD proteins .
Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, ferredoxin-like superfamily (ForMFR_H4MPT_ForTrfase_fd-like)
Type: Homologous_superfamily

Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction:

N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin

Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel β sheet flanked by α helices forming an α/β sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface . Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure .

In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates .

This superfamily represents two ferredoxin-like domains found in Ftr.
L-carnitine/gamma-butyrobetaine antiporter CaiT (BCCT_transptr_CaiT)
Type: Family

CaiT is a membrane antiporter that catalyses the exchange of L-carnitine for gamma-butyrobetaine, which is the excreted end product of the carnitine pathway .

CaiT belongs to a family known as BCCT (for Betaine / Carnitine / Choline Transporters) , which are specific for compounds containing a quaternary nitrogen atom. The BCCT proteins contain 12 transmembrane regionsand are energised by proton symport. They contain a conserved region with four tryptophans in their central region .

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.
Crotonobetainyl-CoA reductase CaiA (CaiA)
Type: Family

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.

The CaiA protein catalyses the irreversible reduction of crotonobetainyl-CoA to gamma-butyrobetainyl-CoA .
Thymidylate synthase/dCMP hydroxymethylase domain (Thymidate_synth/dCMP_Mease_dom)
Type: Domain

Thymidylate synthase (

) catalyzes 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 essential for regulating the balanced supply of the 4 DNA precursors in normal DNA replication: defects in the enzyme activity affecting the regulation process cause various biological and genetic abnormalities, such as thymineless death . The enzyme is an important target for certain chemotherapeutic drugs. Thymidylate synthase is an enzyme of about 30 to 35 Kd in most species except in protozoan and plants where it exists as a bifunctional enzyme that includes a dihydrofolate reductase domain . 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.

Thymidylate synthase also acts as a regulator of its own expression by binding and inactivating its own RNA. Due to its key role in the de novo pathway for thymidylate synthesis and, hence, DNA synthesis, it is one of the most conserved enzymes across species and phyla . Thymidylate synthase is a well-recognized target for anticancer chemotherapy, as well as a valuable new target against infectious diseases . Interestingly, in several protozoa, a single polypeptide chain codes for both dihydrofolate reductase (DHFR) and thymidylate synthase (TS), forming a bifunctional enzyme (DHFR-TS), possibly through gene fusion at a single evolutionary point. DHFR-TS is also active as a dimer .

This entry also includes dUMP hydroxymethylases and dCMP hydroxymethyltransferases from bacteriophages. dCMP-HMase catalyses the reversible conversion of dCMP and CH2THF to hydroxymethyl-dCMP and THF. dUMP hydroxymethylase is encoded by several bacteriophages that infect Bacillus subtilis and contain hydroxymethyl-dUMP instead of dTMP in their DNA, for their own protection against the host restriction system .

dCMP hydroxymethyltransferase has a subunit fold and a dimerisation pattern in common with thymidylate synthases .
L-carnitine CoA-transferase CaiB (CoA-Trfase_CaiB)
Type: Family

CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism:

Family I consists of CoA-transferases for 3-oxoacids (

,

), short-chain fatty acids (

,

) and glutaconate (

). Most use succinyl-CoA or acetyl-CoA as CoA donors.

Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (

,

). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well.

Family III consists of formyl-CoA:oxalate CoA-transferase , succinyl-CoA:(R)-benzylsuccinate CoA-transferase , (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase , succinyl-CoA:mesaconate CoA-transferase and butyrobetainyl-CoA:(R)-carnitine CoA-transferase . These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate-and stereo-specific manner .

CaiB is a family III CoA-transferase that catalyzes the reversible transfer of the CoA moiety from gamma-butyrobetainyl-CoA to L-carnitine to generate L-carnitinyl-CoA and gamma-butyrobetaine . This enzyme can also catalyse the reversible transfer of the CoA moiety from gamma-butyrobetainyl-CoA or L-carnitinyl-CoA to crotonobetaine to generate crotonobetainyl-CoA.
In Escherichia coli, CaiB is one of the genes encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism .
Methionine repressor MetJ domain superfamily (Met_repressor_MetJ_dom_sf)
Type: Homologous_superfamily

Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change . MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated.

MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer .

The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein β-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs .