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Protein

Periplasmic [Fe] hydrogenase large subunit

Gene

hydA

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+.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi35 – 351Iron-sulfur 1 (4Fe-4S)
Metal bindingi38 – 381Iron-sulfur 1 (4Fe-4S)
Metal bindingi41 – 411Iron-sulfur 1 (4Fe-4S)
Metal bindingi45 – 451Iron-sulfur 2 (4Fe-4S)
Metal bindingi66 – 661Iron-sulfur 2 (4Fe-4S)
Metal bindingi69 – 691Iron-sulfur 2 (4Fe-4S)
Metal bindingi72 – 721Iron-sulfur 2 (4Fe-4S)
Metal bindingi76 – 761Iron-sulfur 1 (4Fe-4S)
Metal bindingi179 – 1791Iron-sulfur 3 (4Fe-4S)
Metal bindingi234 – 2341Iron-sulfur 3 (4Fe-4S)
Metal bindingi378 – 3781Iron-sulfur 3 (4Fe-4S)
Metal bindingi382 – 3821Diiron subcluster
Metal bindingi382 – 3821Iron-sulfur 3 (4Fe-4S)

GO - Molecular functioni

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

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciDVUL882:GJIL-1810-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [Fe] hydrogenase large subunit (EC:1.12.7.2)
Alternative name(s):
Fe hydrogenlyase
Gene namesi
Name:hydA
Ordered Locus Names:DVU_1769
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
Chaini1 – 421421Periplasmic [Fe] hydrogenase large subunitPRO_0000159239Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6186N.
STRINGi882.DVU1769.

Structurei

Secondary structure

1
421
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Beta strandi9 – 113Combined sources
Helixi22 – 243Combined sources
Beta strandi27 – 304Combined sources
Turni32 – 343Combined sources
Helixi40 – 445Combined sources
Helixi63 – 653Combined sources
Helixi73 – 753Combined sources
Beta strandi81 – 844Combined sources
Helixi88 – 969Combined sources
Beta strandi101 – 1066Combined sources
Helixi108 – 1125Combined sources
Helixi114 – 1185Combined sources
Helixi127 – 13711Combined sources
Beta strandi140 – 1423Combined sources
Helixi145 – 16420Combined sources
Beta strandi172 – 1754Combined sources
Helixi180 – 18910Combined sources
Helixi191 – 1966Combined sources
Helixi203 – 2119Combined sources
Helixi214 – 2196Combined sources
Helixi223 – 2253Combined sources
Beta strandi226 – 2338Combined sources
Helixi236 – 2416Combined sources
Beta strandi256 – 2594Combined sources
Helixi260 – 26910Combined sources
Helixi274 – 2763Combined sources
Turni284 – 2863Combined sources
Helixi291 – 2944Combined sources
Helixi295 – 2973Combined sources
Helixi301 – 31515Combined sources
Helixi325 – 3273Combined sources
Beta strandi332 – 3409Combined sources
Beta strandi343 – 35210Combined sources
Helixi353 – 3553Combined sources
Helixi356 – 3649Combined sources
Beta strandi371 – 3788Combined sources
Helixi382 – 3843Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E08NMR-A27-397[»]
1GX7NMR-A27-397[»]
1HFEX-ray1.60L/M1-421[»]
DisProtiDP00108.
ProteinModelPortaliP07598.
SMRiP07598. Positions 2-397.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07598.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini26 – 57324Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
BLAST
Domaini59 – 86284Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 2 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG4624.
KOiK00533.
OMAiCTKKECS.
OrthoDBiEOG6CVV7G.
PhylomeDBiP07598.

Family and domain databases

InterProiIPR001450. 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]
PfamiPF02906. Fe_hyd_lg_C. 1 hit.
PF00037. Fer4. 2 hits.
[Graphical view]
SUPFAMiSSF53920. SSF53920. 1 hit.
TIGRFAMsiTIGR02512. FeFe_hydrog_A. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

Sequencei

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
Checksum:i8E70A0775B68AACD
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti35 – 351C → K AA sequence (PubMed:3322275).Curated

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.
RefSeqiYP_010987.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS96246; AAS96246; DVU_1769.
GeneIDi2795816.
KEGGidvu:DVU1769.
PATRICi32063304. VBIDesVul119526_1625.

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.
RefSeqiYP_010987.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E08NMR-A27-397[»]
1GX7NMR-A27-397[»]
1HFEX-ray1.60L/M1-421[»]
DisProtiDP00108.
ProteinModelPortaliP07598.
SMRiP07598. Positions 2-397.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6186N.
STRINGi882.DVU1769.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS96246; AAS96246; DVU_1769.
GeneIDi2795816.
KEGGidvu:DVU1769.
PATRICi32063304. VBIDesVul119526_1625.

Phylogenomic databases

eggNOGiCOG4624.
KOiK00533.
OMAiCTKKECS.
OrthoDBiEOG6CVV7G.
PhylomeDBiP07598.

Enzyme and pathway databases

BioCyciDVUL882:GJIL-1810-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP07598.

Family and domain databases

InterProiIPR001450. 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]
PfamiPF02906. Fe_hyd_lg_C. 1 hit.
PF00037. Fer4. 2 hits.
[Graphical view]
SUPFAMiSSF53920. SSF53920. 1 hit.
TIGRFAMsiTIGR02512. FeFe_hydrog_A. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[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 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.

Entry informationi

Entry nameiPHFL_DESVH
AccessioniPrimary (citable) accession number: P07598
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: January 7, 2015
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

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
  2. SIMILARITY comments
    Index of protein domains and families

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.