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Protein

Periplasmic [Fe] hydrogenase large subunit

Gene

hydA

Organism
Desulfovibrio oxamicus (strain Monticello) (Desulfovibrio vulgaris subsp. oxamicus)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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:
  • [4Fe-4S] clusterBy similarityNote: Binds 3 [4Fe-4S] clusters per subunit.By similarity
  • Fe cationBy similarityNote: Binds 2 iron ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi35Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi38Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi41Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi45Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi66Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi69Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi72Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi76Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi179Iron-sulfur 3 (4Fe-4S)By similarity1
Metal bindingi234Iron-sulfur 3 (4Fe-4S)By similarity1
Metal bindingi378Iron-sulfur 3 (4Fe-4S)By similarity1
Metal bindingi382Diiron subclusterBy similarity1
Metal bindingi382Iron-sulfur 3 (4Fe-4S)By similarity1

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
OrganismiDesulfovibrio oxamicus (strain Monticello) (Desulfovibrio vulgaris subsp. oxamicus)
Taxonomic identifieri884 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001592401 – 421Periplasmic [Fe] hydrogenase large subunitAdd BLAST421

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Structurei

3D structure databases

ProteinModelPortaliP13629.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini26 – 554Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST30
Domaini56 – 864Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST31

Sequence similaritiesi

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

Keywords - Domaini

Repeat

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.
PF13187. Fer4_9. 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.

P13629-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRIEMEKIF YEDHAPDPKA DPDKLFFIQI DESKCIGCDS CQQYCPTGAI
60 70 80 90 100
FGDTGDAHKI PHEELCINCG QCLTHCPVGA IYESQSWVTE IEKKIKAKDV
110 120 130 140 150
KVIAMPAPAV RYALGDAFGL PVGTVTTGKM FSALKELGFD HCWDNEFTAD
160 170 180 190 200
VTIWEEGTEF VQRLTKKLDK PLPQFTSCCP GWHKYVESLY PELFPHMSSC
210 220 230 240 250
KSPIGMLGTL AKTYGADRMK YDRAKVYTVS IMPCTAKKYE GMRPQLWDSG
260 270 280 290 300
HKDIDATIDT RELAYMIKKA KIDFTKLPDG KRDTLMGEST GGATLFGVTG
310 320 330 340 350
GVMEAALRYA YQAVTGKKPE SMDFKGVRGL QGVKEATVNV GGVDVKVAVV
360 370 380 390 400
HGARRFHDVC ELVKAGKAPW HFIEFMACPG GCVCGGGQPV MPGVLEAADR
410 420
RSTRMYAGLK KRLAMASASR A
Length:421
Mass (Da):46,279
Last modified:January 1, 1990 - v1
Checksum:i8E987ABC4DC7C965
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27212 Genomic DNA. Translation: AAA23373.1.
PIRiA32886. HQDVLV.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27212 Genomic DNA. Translation: AAA23373.1.
PIRiA32886. HQDVLV.

3D structure databases

ProteinModelPortaliP13629.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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.
PF13187. Fer4_9. 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_DESOM
AccessioniPrimary (citable) accession number: P13629
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: October 5, 2016
This is version 87 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.

Documents

  1. 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.