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Protein

Periplasmic [NiFe] hydrogenase small subunit

Gene

hydA

Organism
Desulfovibrio fructosivorans
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

Redox potential

E0 is about +65 mV for the 3Fe-4S, and -340 mV for the 4Fe-4S clusters.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi67Iron-sulfur 1 (4Fe-4S)1
Metal bindingi70Iron-sulfur 1 (4Fe-4S)1
Metal bindingi164Iron-sulfur 1 (4Fe-4S)1
Metal bindingi197Iron-sulfur 1 (4Fe-4S)1
Metal bindingi234Iron-sulfur 2 (4Fe-4S); via pros nitrogen1
Metal bindingi237Iron-sulfur 2 (4Fe-4S)1
Metal bindingi262Iron-sulfur 2 (4Fe-4S)1
Metal bindingi268Iron-sulfur 2 (4Fe-4S)1
Metal bindingi277Iron-sulfur 3 (3Fe-4S)1
Metal bindingi295Iron-sulfur 3 (3Fe-4S)1
Metal bindingi298Iron-sulfur 3 (3Fe-4S)1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionOxidoreductase
Ligand3Fe-4S, 4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
1.12.2.1 1906

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Periplasmic [NiFe] hydrogenase small subunit (EC:1.12.2.1)
Alternative name(s):
NiFe hydrogenlyase small chain
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:hydA
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiDesulfovibrio fructosivorans
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri878 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Periplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi238P → C: Decreased hydrogen uptake and increased hydrogen production. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 49Tat-type signalPROSITE-ProRule annotation1 PublicationAdd BLAST49
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000001341550 – 314Periplasmic [NiFe] hydrogenase small subunitAdd BLAST265

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
P18187

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterodimer of a large and a small subunit.2 Publications

Protein-protein interaction databases

Database of interacting proteins

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DIPi
DIP-6172N

Molecular INTeraction database

More...
MINTi
P18187

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1314
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P18187

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P18187

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P18187

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105E3S Bacteria
COG1740 LUCA

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.700, 1 hit
4.10.480.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR027394 Cytochrome-c3_hydrogenase_C
IPR006137 NADH_UbQ_OxRdtase-like_20kDa
IPR037148 NiFe-Hase_small_C_sf
IPR037024 NiFe_Hase_small_N_sf
IPR001821 NiFe_hydrogenase_ssu
IPR006311 TAT_signal
IPR019546 TAT_signal_bac_arc

The PANTHER Classification System

More...
PANTHERi
PTHR30013 PTHR30013, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF14720 NiFe_hyd_SSU_C, 1 hit
PF01058 Oxidored_q6, 1 hit
PF10518 TAT_signal, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF000310 NiFe_hyd_ssu, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00391 hydA, 1 hit
TIGR01409 TAT_signal_seq, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51318 TAT, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P18187-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNFSVGLGRD DAEKRLVQNG VSRRDFMKFC ATVAAAMGMG PAFAPKVAEA
60 70 80 90 100
LTAKHRPSVV WLHNAECTGC TEAAIRTIKP YIDALILDTI SLDYQETIMA
110 120 130 140 150
AAGEAAEAAL HQALEGKDGY YLVVEGGLPT IDGGQWGMVA GHPMIETTKK
160 170 180 190 200
AAAKAKGIIC IGTCSAYGGV QKAKPNPSQA KGVSEALGVK TINIPGCPPN
210 220 230 240 250
PINFVGAVVH VLTKGIPDLD ENGRPKLFYG ELVHDNCPRL PHFEASEFAP
260 270 280 290 300
SFDSEEAKKG FCLYELGCKG PVTYNNCPKV LFNQVNWPVQ AGHPCLGCSE
310
PDFWDTMTPF YEQG
Length:314
Mass (Da):33,621
Last modified:July 22, 2008 - v4
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i48BE00FE51D23A68
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M35333 Genomic DNA Translation: AAA23371.2

Protein sequence database of the Protein Information Resource

More...
PIRi
JQ0761 S08198

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35333 Genomic DNA Translation: AAA23371.2
PIRiJQ0761 S08198

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FRFX-ray2.70S51-161[»]
S163-314[»]
1YQWX-ray1.83A/B/C51-314[»]
1YRQX-ray2.10A/B/C/D/F/G51-314[»]
3CURX-ray2.40A/B/C51-314[»]
3CUSX-ray2.20A/B/C51-314[»]
3H3XX-ray2.70A/B/C51-314[»]
4UCQX-ray2.60A/B/C51-314[»]
4UCWX-ray2.30A/B/C51-314[»]
4UCXX-ray1.95A/B/C51-314[»]
4UE2X-ray2.02A/B/C51-314[»]
4UE6X-ray2.30A/B/C51-314[»]
4UEWX-ray2.08A/B/C51-314[»]
4UPEX-ray1.80A/B/C50-314[»]
4UPVX-ray1.52A/B50-314[»]
4UQLX-ray1.22A/B50-314[»]
4UQPX-ray1.42A/B50-314[»]
4URHX-ray1.44A/B/C50-314[»]
ProteinModelPortaliP18187
SMRiP18187
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6172N
MINTiP18187

Proteomic databases

PRIDEiP18187

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105E3S Bacteria
COG1740 LUCA

Enzyme and pathway databases

BRENDAi1.12.2.1 1906

Miscellaneous databases

EvolutionaryTraceiP18187

Family and domain databases

Gene3Di3.40.50.700, 1 hit
4.10.480.10, 1 hit
InterProiView protein in InterPro
IPR027394 Cytochrome-c3_hydrogenase_C
IPR006137 NADH_UbQ_OxRdtase-like_20kDa
IPR037148 NiFe-Hase_small_C_sf
IPR037024 NiFe_Hase_small_N_sf
IPR001821 NiFe_hydrogenase_ssu
IPR006311 TAT_signal
IPR019546 TAT_signal_bac_arc
PANTHERiPTHR30013 PTHR30013, 1 hit
PfamiView protein in Pfam
PF14720 NiFe_hyd_SSU_C, 1 hit
PF01058 Oxidored_q6, 1 hit
PF10518 TAT_signal, 1 hit
PIRSFiPIRSF000310 NiFe_hyd_ssu, 1 hit
TIGRFAMsiTIGR00391 hydA, 1 hit
TIGR01409 TAT_signal_seq, 1 hit
PROSITEiView protein in PROSITE
PS51318 TAT, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPHNS_DESFR
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P18187
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: July 22, 2008
Last modified: December 5, 2018
This is version 140 of the entry and version 4 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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