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Protein

Periplasmic [Fe] hydrogenase large subunit

Gene

hydA

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / 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)DescriptionActionsGraphical viewLength
Metal bindingi35Iron-sulfur 1 (4Fe-4S)1
Metal bindingi38Iron-sulfur 1 (4Fe-4S)1
Metal bindingi41Iron-sulfur 1 (4Fe-4S)1
Metal bindingi45Iron-sulfur 2 (4Fe-4S)1
Metal bindingi66Iron-sulfur 2 (4Fe-4S)1
Metal bindingi69Iron-sulfur 2 (4Fe-4S)1
Metal bindingi72Iron-sulfur 2 (4Fe-4S)1
Metal bindingi76Iron-sulfur 1 (4Fe-4S)1
Metal bindingi179Iron-sulfur 3 (4Fe-4S)1
Metal bindingi234Iron-sulfur 3 (4Fe-4S)1
Metal bindingi378Iron-sulfur 3 (4Fe-4S)1
Metal bindingi382Diiron subcluster1
Metal bindingi382Iron-sulfur 3 (4Fe-4S)1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

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

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 / DSM 644 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002194 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001592391 – 421Periplasmic [Fe] hydrogenase large subunitAdd BLAST421

Proteomic databases

PaxDbiP07598.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6186N.
STRINGi882.DVU1769.

Structurei

Secondary structure

1421
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 6Combined sources3
Beta strandi9 – 11Combined sources3
Helixi22 – 24Combined sources3
Beta strandi27 – 30Combined sources4
Turni32 – 34Combined sources3
Helixi40 – 44Combined sources5
Helixi63 – 65Combined sources3
Helixi73 – 75Combined sources3
Beta strandi81 – 84Combined sources4
Helixi88 – 96Combined sources9
Beta strandi101 – 106Combined sources6
Helixi108 – 112Combined sources5
Helixi114 – 118Combined sources5
Helixi127 – 137Combined sources11
Beta strandi140 – 142Combined sources3
Helixi145 – 164Combined sources20
Beta strandi172 – 175Combined sources4
Helixi180 – 189Combined sources10
Helixi191 – 196Combined sources6
Helixi203 – 211Combined sources9
Helixi214 – 219Combined sources6
Helixi223 – 225Combined sources3
Beta strandi226 – 233Combined sources8
Helixi236 – 241Combined sources6
Beta strandi256 – 259Combined sources4
Helixi260 – 269Combined sources10
Helixi274 – 276Combined sources3
Turni284 – 286Combined sources3
Helixi291 – 294Combined sources4
Helixi295 – 297Combined sources3
Helixi301 – 315Combined sources15
Helixi325 – 327Combined sources3
Beta strandi332 – 340Combined sources9
Beta strandi343 – 352Combined sources10
Helixi353 – 355Combined sources3
Helixi356 – 364Combined sources9
Beta strandi371 – 378Combined sources8
Helixi382 – 384Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP07598.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini26 – 574Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST32
Domaini59 – 864Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST28

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG4107QHI. Bacteria.
COG4624. LUCA.
KOiK00533.
OMAiENCTKTE.
OrthoDBiPOG091H01RQ.
PhylomeDBiP07598.

Family and domain databases

InterProiIPR017896. 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.
PF13237. Fer4_10. 1 hit.
[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)DescriptionActionsGraphical viewLength
Sequence conflicti35C → K AA sequence (PubMed:3322275).Curated1

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.
RefSeqiWP_010939057.1. NC_002937.3.
YP_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.
RefSeqiWP_010939057.1. NC_002937.3.
YP_010987.1. NC_002937.3.

3D structure databases

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

Protein-protein interaction databases

DIPiDIP-6186N.
STRINGi882.DVU1769.

Proteomic databases

PaxDbiP07598.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4107QHI. Bacteria.
COG4624. LUCA.
KOiK00533.
OMAiENCTKTE.
OrthoDBiPOG091H01RQ.
PhylomeDBiP07598.

Miscellaneous databases

EvolutionaryTraceiP07598.

Family and domain databases

InterProiIPR017896. 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.
PF13237. Fer4_10. 1 hit.
[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...

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: November 2, 2016
This is version 135 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

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 one 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.