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Protein

Periplasmic [NiFe] hydrogenase large subunit

Gene

hydB

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
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

Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.

Miscellaneous

Perhaps the leader of the small subunit serves as a transport vehicle for both subunits.

<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 bindingi62Magnesium1
Metal bindingi81Nickel1
Metal bindingi84Iron1
Metal bindingi84Nickel1
Metal bindingi498Magnesium; via carbonyl oxygen1
Metal bindingi546Nickel1
Metal bindingi549Iron1
Metal bindingi549Nickel1
Metal bindingi552Magnesium; via tele nitrogen1

<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
LigandIron, Magnesium, Metal-binding, Nickel

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
DVUL883:G1GTY-284-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 [NiFe] hydrogenase large subunit (EC:1.12.2.1)
Alternative name(s):
NiFe hydrogenlyase large 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:hydB
Ordered Locus Names:DvMF_0270
<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 Miyazaki F / DSM 19637)
<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 identifieri883 [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
  • UP000001361 <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_00000134051 – 552Periplasmic [NiFe] hydrogenase large subunitAdd BLAST552
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes a propeptide, which is a part of a protein that is cleaved during maturation or activation. Once cleaved, a propeptide generally has no independent biological function.<p><a href='/help/propep' target='_top'>More...</a></p>PropeptideiPRO_0000013406553 – 567Add BLAST15

<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-41378N

Protein interaction database and analysis system

More...
IntActi
P21852, 1 interactor

Molecular INTeraction database

More...
MINTi
P21852

STRING: functional protein association networks

More...
STRINGi
883.DvMF_0270

<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

1567
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...
SMRi
P21852

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
P21852

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DPX Bacteria
COG0374 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000278799

KEGG Orthology (KO)

More...
KOi
K00437

Identification of Orthologs from Complete Genome Data

More...
OMAi
EEVTHSW

Database of Orthologous Groups

More...
OrthoDBi
POG091H05OW

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.645.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001501 Ni-dep_hyd_lsu
IPR018194 Ni-dep_hyd_lsu_Ni_BS
IPR029014 NiFe-Hase_large

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00374 NiFeSe_Hases, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF56762 SSF56762, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00507 NI_HGENASE_L_1, 1 hit
PS00508 NI_HGENASE_L_2, 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.

P21852-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSGCRAQNAP GGIPVTPKSS YSGPIVVDPV TRIEGHLRIE VEVENGKVKN
60 70 80 90 100
AYSSSTLFRG LEIILKGRDP RDAQHFTQRT CGVCTYTHAL ASTRCVDNAV
110 120 130 140 150
GVHIPKNATY IRNLVLGAQY LHDHIVHFYH LHALDFVDVT AALKADPAKA
160 170 180 190 200
AKVASSISPR KTTAADLKAV QDKLKTFVES GQLGPFTNAY FLGGHPAYYL
210 220 230 240 250
DPETNLIATA HYLEALRLQV KAARAMAVFG AKNPHTQFTV VGGVTCYDAL
260 270 280 290 300
TPQRIAEFEA LWKETKAFVD EVYIPDLLVV AAAYKDWTQY GGTDNFITFG
310 320 330 340 350
EFPKDEYDLN SRFFKPGVVF KRDFKNIKPF DKMQIEEHVR HSWYEGAEAR
360 370 380 390 400
HPWKGQTQPK YTDLHGDDRY SWMKAPRYMG EPMETGPLAQ VLIAYSQGHP
410 420 430 440 450
KVKAVTDAVL AKLGVGPEAL FSTLGRTAAR GIETAVIAEY VGVMLQEYKD
460 470 480 490 500
NIAKGDNVIC APWEMPKQAE GVGFVNAPRG GLSHWIRIED GKIGNFQLVV
510 520 530 540 550
PSTWTLGPRC DKNKLSPVEA SLIGTPVADA KRPVEILRTV HSFDPCIACG
560
VHVIDGHTNE VHKFRIL
Length:567
Mass (Da):62,641
Last modified:April 14, 2009 - v2
<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:i8BE92277C0E46FDA
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 conflicti180S → T in AAA23370 (PubMed:2269874).Curated1
Sequence conflicti514 – 515KL → NV in AAA23370 (PubMed:2269874).Curated2

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
M58339 Genomic DNA Translation: AAA23370.1
CP001197 Genomic DNA Translation: ACL07227.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B45865

NCBI Reference Sequences

More...
RefSeqi
WP_012611421.1, NC_011769.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ACL07227; ACL07227; DvMF_0270

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
dvm:DvMF_0270

<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
M58339 Genomic DNA Translation: AAA23370.1
CP001197 Genomic DNA Translation: ACL07227.1
PIRiB45865
RefSeqiWP_012611421.1, NC_011769.1

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
1H2AX-ray1.80L1-567[»]
1H2RX-ray1.40L19-552[»]
1UBHX-ray1.35L19-552[»]
1UBJX-ray1.35L19-552[»]
1UBKX-ray1.18L19-552[»]
1UBLX-ray1.20L19-552[»]
1UBMX-ray1.40L19-552[»]
1UBOX-ray1.35L19-552[»]
1UBRX-ray1.34L19-552[»]
1UBTX-ray1.34L19-552[»]
1UBUX-ray1.35L19-552[»]
1WUHX-ray1.24L19-552[»]
1WUIX-ray1.04L19-552[»]
1WUJX-ray1.40L19-552[»]
1WUKX-ray1.10L19-552[»]
1WULX-ray1.50L19-552[»]
4U9HX-ray0.89L20-552[»]
4U9IX-ray1.06L20-552[»]
5XLEX-ray1.69L1-552[»]
5XLFX-ray1.71L1-552[»]
5XLGX-ray1.64L1-552[»]
5XLHX-ray1.93L1-552[»]
5Y4NX-ray1.69L1-552[»]
SMRiP21852
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-41378N
IntActiP21852, 1 interactor
MINTiP21852
STRINGi883.DvMF_0270

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL07227; ACL07227; DvMF_0270
KEGGidvm:DvMF_0270

Phylogenomic databases

eggNOGiENOG4105DPX Bacteria
COG0374 LUCA
HOGENOMiHOG000278799
KOiK00437
OMAiEEVTHSW
OrthoDBiPOG091H05OW

Enzyme and pathway databases

BioCyciDVUL883:G1GTY-284-MONOMER

Miscellaneous databases

EvolutionaryTraceiP21852

Family and domain databases

Gene3Di1.10.645.10, 1 hit
InterProiView protein in InterPro
IPR001501 Ni-dep_hyd_lsu
IPR018194 Ni-dep_hyd_lsu_Ni_BS
IPR029014 NiFe-Hase_large
PfamiView protein in Pfam
PF00374 NiFeSe_Hases, 1 hit
SUPFAMiSSF56762 SSF56762, 1 hit
PROSITEiView protein in PROSITE
PS00507 NI_HGENASE_L_1, 1 hit
PS00508 NI_HGENASE_L_2, 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 nameiPHNL_DESVM
<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: P21852
Secondary accession number(s): B8DPE0
<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: May 1, 1991
Last sequence update: April 14, 2009
Last modified: December 5, 2018
This is version 122 of the entry and version 2 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, Reference proteome

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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