Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Periplasmic [Fe] hydrogenase large subunit

Gene

hydA

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
Status
Reviewed-Annotation score:

Annotation score:4 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

May be involved in hydrogen uptake for the reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is likely to be the physiological electron carrier for the enzyme.

Miscellaneous

[Fe], [NiFe], and [NiFeSe] hydrogenases appear to represent three distinct enzymes having hydrogenase activity.

<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:

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 bindingi35Iron-sulfur 1 (4Fe-4S)1
Metal bindingi38Iron-sulfur 1 (4Fe-4S)1
Metal bindingi41Iron-sulfur 1 (4Fe-4S)1
Metal bindingi45Iron-sulfur 2 (4Fe-4S)1
Metal bindingi66Iron-sulfur 2 (4Fe-4S)1
Metal bindingi69Iron-sulfur 2 (4Fe-4S)1
Metal bindingi72Iron-sulfur 2 (4Fe-4S)1
Metal bindingi76Iron-sulfur 1 (4Fe-4S)1
Metal bindingi179Iron-sulfur 3 (4Fe-4S)1
Metal bindingi234Iron-sulfur 3 (4Fe-4S)1
Metal bindingi378Iron-sulfur 3 (4Fe-4S)1
Metal bindingi382Diiron subcluster1
Metal bindingi382Iron-sulfur 3 (4Fe-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
Biological processElectron transport, Transport
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
DVUL882:G1GT1-1817-MONOMER

<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 [Fe] hydrogenase large subunit (EC:1.12.7.2)
Alternative name(s):
Fe hydrogenlyase
<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
Ordered Locus Names:DVU_1769
<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 vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
<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 identifieri882 [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 subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002194 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<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 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 describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001592391 – 421Periplasmic [Fe] hydrogenase large subunitAdd BLAST421

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P07598

<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.

Protein-protein interaction databases

Database of interacting proteins

More...
DIPi
DIP-6186N

Protein interaction database and analysis system

More...
IntActi
P07598, 1 interactor

STRING: functional protein association networks

More...
STRINGi
882.DVU1769

<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

1421
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Database of protein disorder

More...
DisProti
DP00108

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
P07598

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

More...
SMRi
P07598

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
P07598

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini26 – 574Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST32
Domaini59 – 864Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST28

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4107QHI Bacteria
COG4624 LUCA

KEGG Orthology (KO)

More...
KOi
K00533

Identification of Orthologs from Complete Genome Data

More...
OMAi
CFDDTNC

Database of Orthologous Groups

More...
OrthoDBi
POG091H01RQ

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P07598

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR017896 4Fe4S_Fe-S-bd
IPR017900 4Fe4S_Fe_S_CS
IPR009016 Fe_hydrogenase
IPR004108 Fe_hydrogenase_lsu_C
IPR013352 Fe_hydrogenase_subset

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02906 Fe_hyd_lg_C, 1 hit
PF13237 Fer4_10, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53920 SSF53920, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02512 FeFe_hydrog_A, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00198 4FE4S_FER_1, 2 hits
PS51379 4FE4S_FER_2, 2 hits

<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.

P07598-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSRTVMERIE YEMHTPDPKA DPDKLHFVQI DEAKCIGCDT CSQYCPTAAI
60 70 80 90 100
FGEMGEPHSI PHIEACINCG QCLTHCPENA IYEAQSWVPE VEKKLKDGKV
110 120 130 140 150
KCIAMPAPAV RYALGDAFGM PVGSVTTGKM LAALQKLGFA HCWDTEFTAD
160 170 180 190 200
VTIWEEGSEF VERLTKKSDM PLPQFTSCCP GWQKYAETYY PELLPHFSTC
210 220 230 240 250
KSPIGMNGAL AKTYGAERMK YDPKQVYTVS IMPCIAKKYE GLRPELKSSG
260 270 280 290 300
MRDIDATLTT RELAYMIKKA GIDFAKLPDG KRDSLMGEST GGATIFGVTG
310 320 330 340 350
GVMEAALRFA YEAVTGKKPD SWDFKAVRGL DGIKEATVNV GGTDVKVAVV
360 370 380 390 400
HGAKRFKQVC DDVKAGKSPY HFIEYMACPG GCVCGGGQPV MPGVLEAMDR
410 420
TTTRLYAGLK KRLAMASANK A
Length:421
Mass (Da):45,951
Last modified:April 1, 1988 - v1
<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:i8E70A0775B68AACD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti35C → K AA sequence (PubMed:3322275).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
X02416 Genomic DNA Translation: CAA26266.1
AE017285 Genomic DNA Translation: AAS96246.1
Z15142 Genomic DNA Translation: CAA78848.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A24551 HQDVFL

NCBI Reference Sequences

More...
RefSeqi
WP_010939057.1, NC_002937.3
YP_010987.1, NC_002937.3

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAS96246; AAS96246; DVU_1769

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
2795816

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
dvu:DVU1769

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|882.5.peg.1625

<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
X02416 Genomic DNA Translation: CAA26266.1
AE017285 Genomic DNA Translation: AAS96246.1
Z15142 Genomic DNA Translation: CAA78848.1
PIRiA24551 HQDVFL
RefSeqiWP_010939057.1, NC_002937.3
YP_010987.1, NC_002937.3

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
1E08NMR-A27-397[»]
1GX7NMR-A27-397[»]
1HFEX-ray1.60L/M1-421[»]
DisProtiDP00108
ProteinModelPortaliP07598
SMRiP07598
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6186N
IntActiP07598, 1 interactor
STRINGi882.DVU1769

Proteomic databases

PaxDbiP07598

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS96246; AAS96246; DVU_1769
GeneIDi2795816
KEGGidvu:DVU1769
PATRICifig|882.5.peg.1625

Phylogenomic databases

eggNOGiENOG4107QHI Bacteria
COG4624 LUCA
KOiK00533
OMAiCFDDTNC
OrthoDBiPOG091H01RQ
PhylomeDBiP07598

Enzyme and pathway databases

BioCyciDVUL882:G1GT1-1817-MONOMER

Miscellaneous databases

EvolutionaryTraceiP07598

Family and domain databases

InterProiView protein in InterPro
IPR017896 4Fe4S_Fe-S-bd
IPR017900 4Fe4S_Fe_S_CS
IPR009016 Fe_hydrogenase
IPR004108 Fe_hydrogenase_lsu_C
IPR013352 Fe_hydrogenase_subset
PfamiView protein in Pfam
PF02906 Fe_hyd_lg_C, 1 hit
PF13237 Fer4_10, 1 hit
SUPFAMiSSF53920 SSF53920, 1 hit
TIGRFAMsiTIGR02512 FeFe_hydrog_A, 1 hit
PROSITEiView protein in PROSITE
PS00198 4FE4S_FER_1, 2 hits
PS51379 4FE4S_FER_2, 2 hits

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 nameiPHFL_DESVH
<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: P07598
<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: April 1, 1988
Last sequence update: April 1, 1988
Last modified: December 5, 2018
This is version 141 of the entry and version 1 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, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again