SII-SWORD/CoKE huggingface dataset:
Photosystem II cytochrome b559, N-terminal (PSII_cyt_b559_N)
Type: Domain

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 .

Cytochrome b559, which forms part of the reaction centre core of PSII is 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 .

This domain occurs in both the alpha and beta subunits of cytochrome B559. In the alpha subunit it occurs together with a lumenal domain (

), while in the beta subunit it occurs on its own.
Photosystem II cytochrome b559, alpha subunit, lumenal region (PSII_cytb559_asu_lum)
Type: Domain

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 .

The alpha subunit (PsbE) of cytochrome b559, 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 .

This domain occurs in the lumenal region of the alpha subunit. It is usually found in conjuction with an N-terminal domain (

).
Zinc finger, RING/FYVE/PHD-type (Znf_RING/FYVE/PHD)
Type: Homologous_superfamily

This superfamily represents RING-, PHD-, and FYVE-type zinc finger domains, which share a common dimetal (zinc)-bound α/β structural fold, as well as the non-zinc-containing U-box domain, which is similar to the RING zinc finger only lacking the metal ion-binding residues (U-box associated with multi-ubiquitination).

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Sodium:neurotransmitter symporter, serotonin, N-terminal (Na/ntran_symport_serotonin_N)
Type: Domain

The serotonin (5-HT) neurotransmitter transporter is known to be expressed in the brain and also in the periphery: on platelet, placental and pulmonary cell membranes. The brain 5-HT transporter is thought to be the principal site of action of therapeutic anti-depressants (which inhibit this transporter), and it may also mediate the behavioural effects of cocaine and amphetamines . The human form (630 amino acids) is 92% identical to the rat brain 5-HT transporter, and shares the same predicted topology and conserved sites for post-translational modification.

This domain is found at the N-terminal region of some 5-HT neurotransmitters.

Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions . Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na
+
and Cl
-
, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na
+
and the counter-transport of K
+
, with no apparent dependence on Cl
-
. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters .
Zinc finger C2H2-type (Znf_C2H2_type)
Type: Domain

This entry represents the classical C2H2 zinc finger domain.

C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β-hairpin and an α-helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 . C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes . Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA . C2H2 zinc fingers can also bind to RNA and protein targets .

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Zinc finger, NHR/GATA-type (Znf_NHR/GATA)
Type: Homologous_superfamily

This entry represents a zinc finger motif found in nuclear hormone receptors and in erythroid transcription factor GATA-1. Nuclear hormone receptors usually have two copies of this motif, while GATA-1 has one copy. The zinc fingers in nuclear receptors are generally regarded as DNA-binding domains , while those in GATA-1 have been implicated in protein-recognition (of FOG proteins) .

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Alpha/beta hydrolase fold-3 (AB_hydrolase_3)
Type: Domain

This entry represents the catalytic domain fold-3 of α/β hydrolase.

The α/β hydrolase fold is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is an α/β-sheet (rather than a barrel), containing 8 strands connected by helices . The enzymes are believed to have diverged from a common ancestor, preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best conserved structural features of the fold. Esterase (EST) from Pseudomonas putida is a member of the α/β hydrolase fold superfamily of enzymes .

In most of the family members the β-strands are parallel, but some have an inversion of the first strands, which gives it an antiparallel orientation. The catalytic triad residues are presented on loops. One of these is the nucleophile elbow and is the most conserved feature of the fold. Some other members lack one or all of the catalytic residues. Some members are therefore inactive but others are involved in surface recognition. The ESTHER database gathers and annotates all the published information related to gene and protein sequences of this superfamily .
Type III secretion system chaperone (T3SS_chaperone)
Type: Family

Type III secretion chaperones are involved in delivering virulence effector proteins from bacterial pathogens directly into eukaryotic cells. The chaperones may prevent aggregation and degradation of their substrates, may target the effector to the secretion apparatus, and may ensure a secretion-component unfolded conformation of their specific substrate. One member of this family, SigE (

) forms homodimers in crystal. The monomers have a novel fold with an α-β(3)-α-β(2)-α topology .
Cupin 2, conserved barrel (Cupin_2)
Type: Domain

This entry represents the conserved barrel domain of the cupin superfamily (cupa is the Latin term for a small barrel).
Stress responsive alpha+beta-barrel (Dabb)
Type: Domain

The stress-response A/B barrel domain is found in a class of stress-response proteins in plants. It is also found in some bacterial fructose-bisphosphate aldolase such as at the C terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (

) .

is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine.

The stress-response A/B barrel domain forms a very stable dimer. This dimer belongs to the superfamily of dimeric α+β barrels in which the two β-sheets form a β-barrel. The two molecules in the dimer are related by a 2-fold axis parallel to helix H1 and β-strands B3 and B4. C-terminal residues extending from the beta4 strand of each monomer wrap around and connect with the beta2 strand and alpha1 helix of the opposing monomer to form the dimer interface .The outer surface of the β-sheets of the two molecules forms a β-barrel-like structure defining a central pore.

The function of the stress-response A/B barrel domain is unknown , but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar) .

Some proteins known to contain a stress response A/B barrel domain are listed below:

Arabidopsis thaliana At3g17210

Arabidopsis thaliana At5g22580

Populus tremula stable protein 1 (SP-1)(Populus species), a thermostable stress-responsive protein.

Pseudomonas hydrogenothermophila fructose 1,6-bisphosphate aldolase (cbbA).

The structure of one of these proteins has been solved (

) and the domain forms an α-β barrel dimer .
Immunoglobulin I-set (Ig_I-set)
Type: Domain

This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 , the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis and the Zwei Ig domain proteins zig involved in the postembriogenic neuronal soma and axon position maintenance .

The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable;

), C1-set (constant-1;

), C2-set (constant-2;

) and I-set (intermediate;

) . Structural studies have shown that these domains share a common core Greek-key β-sandwich structure, with the types differing in the number of strands in the β-sheets as well as in their sequence patterns .

Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system .
Potassium channel domain (K_chnl_dom)
Type: Domain

This domain is found in a variety of potassium channel proteins, including the two membrane helix type ion channels found in bacteria .
Limonene-1,2-epoxide hydrolase (LEH)
Type: Domain

Epoxide hydrolases catalyse the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed β-sheet, with three N-terminal α helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzymes active site .
Phosphate response ubiquitin E3 ligase 1-like, LRR (LRR_PRU1-like)
Type: Repeat

This entry represents a short segment of LRRs found in plant proteins such as Phosphate response ubiquitin E3 ligase 1, PRU1 (also known as Putative F-box/LRR-repeat protein At3g42770). PRU1 is a E3 ligase involved in phosphate homeostasis. Under low Pi stress it targets WRKY6 (AT1G62300) for degradation which in turn is a repressor of PHO1 (AT3G23430) .

Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape . LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions .Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response .

Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel β sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the β-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins.
3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with α-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions . Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20-to 30-residue repeats .
Pyrimidine nucleoside phosphorylase, C-terminal (PYNP_C)
Type: Domain

This domain is found at the C-terminal end of the large α/β domain making up various pyrimidine nucleoside phosphorylases . It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP,

) there is an added three-stranded anti-parallel β sheet as compared to other members of the family, such as Escherichia coli thymidine phosphorylase (TP,

) . The domain contains an α/β hammerhead fold and residues in this domain seem to be important in formation of the homodimer .
Reverse transcriptase, RNA-dependent DNA polymerase (RVT_2)
Type: Domain

A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This entry includes reverse transcriptases not recognised by

.
Clostridium neurotoxin, receptor-binding C-terminal (Toxin_rcpt-bd_C)
Type: Domain

The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (

), the central translocation domains and two receptor-binding domains . This domain is the C-terminal receptor-binding domain, which adopts a modified β-trefoil fold with a six stranded β-barrel and a β-hairpin triplet capping the domain . The first step in the intoxication process is a binding event between this domain and the pre-synaptic nerve ending .