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P07598 (PHFL_DESVH) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 122. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Periplasmic [Fe] hydrogenase large subunit

EC=1.12.7.2
Alternative name(s):
Fe hydrogenlyase
Gene names
Name:hydA
Ordered Locus Names:DVU_1769
OrganismDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) [Reference proteome] [HAMAP]
Taxonomic identifier882 [NCBI]
Taxonomic lineageBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Protein attributes

Sequence length421 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Cofactor

Binds 3 4Fe-4S clusters per subunit.

Binds 2 iron ions per subunit.

Subunit structure

Heterodimer of a large and a small subunit.

Subcellular location

Periplasm.

Miscellaneous

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

Sequence similarities

Contains 2 4Fe-4S ferredoxin-type domains.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 421421Periplasmic [Fe] hydrogenase large subunit
PRO_0000159239

Regions

Domain26 – 57324Fe-4S ferredoxin-type 1
Domain59 – 86284Fe-4S ferredoxin-type 2

Sites

Metal binding351Iron-sulfur 1 (4Fe-4S)
Metal binding381Iron-sulfur 1 (4Fe-4S)
Metal binding411Iron-sulfur 1 (4Fe-4S)
Metal binding451Iron-sulfur 2 (4Fe-4S)
Metal binding661Iron-sulfur 2 (4Fe-4S)
Metal binding691Iron-sulfur 2 (4Fe-4S)
Metal binding721Iron-sulfur 2 (4Fe-4S)
Metal binding761Iron-sulfur 1 (4Fe-4S)
Metal binding1791Iron-sulfur 3 (4Fe-4S)
Metal binding2341Iron-sulfur 3 (4Fe-4S)
Metal binding3781Iron-sulfur 3 (4Fe-4S)
Metal binding3821Diiron subcluster
Metal binding3821Iron-sulfur 3 (4Fe-4S)

Experimental info

Sequence conflict351C → K AA sequence Ref.3

Secondary structure

........................................................................ 421
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P07598 [UniParc].

Last modified April 1, 1988. Version 1.
Checksum: 8E70A0775B68AACD

FASTA42145,951
        10         20         30         40         50         60 
MSRTVMERIE YEMHTPDPKA DPDKLHFVQI DEAKCIGCDT CSQYCPTAAI FGEMGEPHSI 

        70         80         90        100        110        120 
PHIEACINCG QCLTHCPENA IYEAQSWVPE VEKKLKDGKV KCIAMPAPAV RYALGDAFGM 

       130        140        150        160        170        180 
PVGSVTTGKM LAALQKLGFA HCWDTEFTAD VTIWEEGSEF VERLTKKSDM PLPQFTSCCP 

       190        200        210        220        230        240 
GWQKYAETYY PELLPHFSTC KSPIGMNGAL AKTYGAERMK YDPKQVYTVS IMPCIAKKYE 

       250        260        270        280        290        300 
GLRPELKSSG MRDIDATLTT RELAYMIKKA GIDFAKLPDG KRDSLMGEST GGATIFGVTG 

       310        320        330        340        350        360 
GVMEAALRFA YEAVTGKKPD SWDFKAVRGL DGIKEATVNV GGTDVKVAVV HGAKRFKQVC 

       370        380        390        400        410        420 
DDVKAGKSPY HFIEYMACPG GCVCGGGQPV MPGVLEAMDR TTTRLYAGLK KRLAMASANK 


A 

« Hide

References

« Hide 'large scale' references
[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]"The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough."
Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T., Kolonay J.F., Eisen J.A., Ward N.L., Methe B.A., Brinkac L.M., Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Fouts D.E. expand/collapse author list , Haft D.H., Selengut J., Peterson J.D., Davidsen T.M., Zafar N., Zhou L., Radune D., Dimitrov G., Hance M., Tran K., Khouri H.M., Gill J., Utterback T.R., Feldblyum T.V., Wall J.D., Voordouw G., Fraser C.M.
Nat. Biotechnol. 22:554-559(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
[3]"Identification of three classes of hydrogenase in the genus, Desulfovibrio."
Prickril B.C., He S.H., Li C., Menon N.K., Choi E.S., Przybyla A.E., Dervartanian D.V., Peck H.D. Jr., Fauque G., le Gall J., Teixeira M., Moura I., Moura J.J.G., Patil D., Huynh B.H.
Biochem. Biophys. Res. Commun. 149:369-377(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-35.
[4]van den Berg W.A.M., Stokkermans J.P.W.G., van Dongen W.M.A.M.
Submitted (SEP-1992) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-15.
[5]"Mossbauer characterization of the iron-sulfur clusters in Desulfovibrio vulgaris hydrogenase."
Pereira A.S., Tavares P., Moura I., Moura J.J.G., Huynh B.H.
J. Am. Chem. Soc. 123:2771-2782(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: MOSSBAUER SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
[6]"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).
[7]"Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans."
Nicolet Y., de Lacey A.L., Vernede X., Fernandez V.M., Hatchikian E.C., Fontecilla-Camps J.-C.
J. Am. Chem. Soc. 123:1596-1601(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), ABSORPTION SPECTROSCOPY, EPR SPECTROSCOPY, FOURIER-TRANSFORM INFRARED SPECTROSCOPY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X02416 Genomic DNA. Translation: CAA26266.1.
AE017285 Genomic DNA. Translation: AAS96246.1.
Z15142 Genomic DNA. Translation: CAA78848.1.
PIRHQDVFL. A24551.
RefSeqYP_010987.1. NC_002937.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1E08NMR-A27-397[»]
1GX7NMR-A27-397[»]
1HFEX-ray1.60L/M1-421[»]
DisProtDP00108.
ProteinModelPortalP07598.
SMRP07598. Positions 2-397.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-6186N.
STRING882.DVU1769.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAS96246; AAS96246; DVU_1769.
GeneID2795816.
KEGGdvu:DVU1769.
PATRIC32063304. VBIDesVul119526_1625.

Phylogenomic databases

eggNOGCOG4624.
KOK00533.
OMAIFTVSVM.
OrthoDBEOG6CVV7G.
PhylomeDBP07598.

Enzyme and pathway databases

BioCycDVUL882:GJIL-1810-MONOMER.

Family and domain databases

InterProIPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR009016. Fe_hydrogenase.
IPR004108. Fe_hydrogenase_lsu_C.
IPR013352. Fe_hydrogenase_subset.
[Graphical view]
PfamPF02906. Fe_hyd_lg_C. 1 hit.
PF00037. Fer4. 2 hits.
[Graphical view]
SUPFAMSSF53920. SSF53920. 1 hit.
TIGRFAMsTIGR02512. FeFe_hydrog_A. 1 hit.
PROSITEPS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP07598.

Entry information

Entry namePHFL_DESVH
AccessionPrimary (citable) accession number: P07598
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: July 9, 2014
This is version 122 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references