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P07598

- PHFL_DESVH

UniProt

P07598 - PHFL_DESVH

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Protein
Periplasmic [Fe] hydrogenase large subunit
Gene
hydA, DVU_1769
Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed - 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

Binds 3 4Fe-4S clusters per subunit.
Binds 2 iron ions per subunit.

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 subunit
PRO_0000159239Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6186N.
STRINGi882.DVU1769.

Structurei

Secondary structure

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

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP07598.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG4624.
KOiK00533.
OMAiIFTVSVM.
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

MSRTVMERIE YEMHTPDPKA DPDKLHFVQI DEAKCIGCDT CSQYCPTAAI    50
FGEMGEPHSI PHIEACINCG QCLTHCPENA IYEAQSWVPE VEKKLKDGKV 100
KCIAMPAPAV RYALGDAFGM PVGSVTTGKM LAALQKLGFA HCWDTEFTAD 150
VTIWEEGSEF VERLTKKSDM PLPQFTSCCP GWQKYAETYY PELLPHFSTC 200
KSPIGMNGAL AKTYGAERMK YDPKQVYTVS IMPCIAKKYE GLRPELKSSG 250
MRDIDATLTT RELAYMIKKA GIDFAKLPDG KRDSLMGEST GGATIFGVTG 300
GVMEAALRFA YEAVTGKKPD SWDFKAVRGL DGIKEATVNV GGTDVKVAVV 350
HGAKRFKQVC DDVKAGKSPY HFIEYMACPG GCVCGGGQPV MPGVLEAMDR 400
TTTRLYAGLK KRLAMASANK A 421
Length:421
Mass (Da):45,951
Last modified:April 1, 1988 - v1
Checksum:i8E70A0775B68AACD
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti35 – 351C → K AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
X02416 Genomic DNA. Translation: CAA26266.1 .
AE017285 Genomic DNA. Translation: AAS96246.1 .
Z15142 Genomic DNA. Translation: CAA78848.1 .
PIRi A24551. HQDVFL.
RefSeqi YP_010987.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1E08 NMR - A 27-397 [» ]
1GX7 NMR - A 27-397 [» ]
1HFE X-ray 1.60 L/M 1-421 [» ]
DisProti DP00108.
ProteinModelPortali P07598.
SMRi P07598. Positions 2-397.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6186N.
STRINGi 882.DVU1769.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAS96246 ; AAS96246 ; DVU_1769 .
GeneIDi 2795816.
KEGGi dvu:DVU1769.
PATRICi 32063304. VBIDesVul119526_1625.

Phylogenomic databases

eggNOGi COG4624.
KOi K00533.
OMAi IFTVSVM.
OrthoDBi EOG6CVV7G.
PhylomeDBi P07598.

Enzyme and pathway databases

BioCyci DVUL882:GJIL-1810-MONOMER.

Miscellaneous databases

EvolutionaryTracei P07598.

Family and domain databases

InterProi IPR001450. 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 ]
Pfami PF02906. Fe_hyd_lg_C. 1 hit.
PF00037. Fer4. 2 hits.
[Graphical view ]
SUPFAMi SSF53920. SSF53920. 1 hit.
TIGRFAMsi TIGR02512. FeFe_hydrog_A. 1 hit.
PROSITEi PS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view ]
ProtoNeti Search...

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: July 9, 2014
This is version 122 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

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