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Protein

Periplasmic [Fe] hydrogenase small subunit

Gene

hydB

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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.

Catalytic activityi

H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+.

GO - Molecular functioni

  1. electron carrier activity Source: InterPro
  2. ferredoxin hydrogenase activity Source: UniProtKB-EC
  3. iron ion binding Source: InterPro
  4. iron-sulfur cluster binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciDVUL882:GJIL-1811-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [Fe] hydrogenase small subunit (EC:1.12.7.2)
Alternative name(s):
Fe hydrogenlyase small chain
Gene namesi
Name:hydB
Ordered Locus Names:DVU_1770
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000002194: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3434Tat-type signal2 PublicationsPROSITE-ProRule annotationAdd
BLAST
Chaini35 – 12389Periplasmic [Fe] hydrogenase small subunitPRO_0000013413Add
BLAST

Post-translational modificationi

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

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6187N.
STRINGi882.DVU1770.

Structurei

Secondary structure

1
123
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi39 – 5618Combined sources
Helixi62 – 643Combined sources
Helixi66 – 749Combined sources
Helixi82 – 887Combined sources
Helixi97 – 1048Combined sources
Helixi113 – 1164Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E08NMR-D36-123[»]
1GX7NMR-D36-123[»]
1HFEX-ray1.60S/T1-123[»]
ProteinModelPortaliP07603.
SMRiP07603. Positions 36-123.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07603.

Family & Domainsi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiNOG282997.
KOiK00534.
OMAiRVSHANP.
OrthoDBiEOG6GTZMV.

Family and domain databases

Gene3Di4.10.260.20. 1 hit.
InterProiIPR008953. Fe_hydrogenase_ssu.
IPR003149. Fe_hydrogenase_ssu-like.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view]
PfamiPF02256. Fe_hyd_SSU. 1 hit.
[Graphical view]
SMARTiSM00902. Fe_hyd_SSU. 1 hit.
[Graphical view]
SUPFAMiSSF48674. SSF48674. 1 hit.
TIGRFAMsiTIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P07603-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQIASITRRG FLKVACVTTG AALIGIRMTG KAVAAVKQIK DYMLDRINGV
60 70 80 90 100
YGADAKFPVR ASQDNTQVKA LYKSYLEKPL GHKSHDLLHT HWFDKSKGVK
110 120
ELTTAGKLPN PRASEFEGPY PYE
Length:123
Mass (Da):13,624
Last modified:April 1, 1988 - v1
Checksum:i2F4F7A4304ECD47B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02416 Genomic DNA. Translation: CAA26267.1.
AE017285 Genomic DNA. Translation: AAS96247.1.
PIRiB24551. HQDVFS.
RefSeqiYP_010988.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS96247; AAS96247; DVU_1770.
GeneIDi2795817.
KEGGidvu:DVU1770.
PATRICi32063306. VBIDesVul119526_1626.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02416 Genomic DNA. Translation: CAA26267.1.
AE017285 Genomic DNA. Translation: AAS96247.1.
PIRiB24551. HQDVFS.
RefSeqiYP_010988.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E08NMR-D36-123[»]
1GX7NMR-D36-123[»]
1HFEX-ray1.60S/T1-123[»]
ProteinModelPortaliP07603.
SMRiP07603. Positions 36-123.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6187N.
STRINGi882.DVU1770.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS96247; AAS96247; DVU_1770.
GeneIDi2795817.
KEGGidvu:DVU1770.
PATRICi32063306. VBIDesVul119526_1626.

Phylogenomic databases

eggNOGiNOG282997.
KOiK00534.
OMAiRVSHANP.
OrthoDBiEOG6GTZMV.

Enzyme and pathway databases

BioCyciDVUL882:GJIL-1811-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP07603.

Family and domain databases

Gene3Di4.10.260.20. 1 hit.
InterProiIPR008953. Fe_hydrogenase_ssu.
IPR003149. Fe_hydrogenase_ssu-like.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view]
PfamiPF02256. Fe_hyd_SSU. 1 hit.
[Graphical view]
SMARTiSM00902. Fe_hyd_SSU. 1 hit.
[Graphical view]
SUPFAMiSSF48674. SSF48674. 1 hit.
TIGRFAMsiTIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough)."
    Voordouw G., Brenner S.
    Eur. J. Biochem. 148:515-520(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
  3. Cited for: PROTEIN SEQUENCE OF 35-69.
  4. "Putative signal peptide on the small subunit of the periplasmic hydrogenase from Desulfovibrio vulgaris."
    Prickril B.C., Czechowski M.H., Przybyla A.E., Peck H.D. Jr., le Gall J.
    J. Bacteriol. 167:722-725(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIGNAL SEQUENCE CLEAVAGE SITE.
  5. "Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center."
    Nicolet Y., Piras C., Legrand P., Hatchikian E.C., Fontecilla-Camps J.-C.
    Structure 7:13-23(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

Entry informationi

Entry nameiPHFS_DESVH
AccessioniPrimary (citable) accession number: P07603
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: January 7, 2015
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

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

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.