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Protein

Periplasmic [NiFe] hydrogenase small subunit

Gene

hydA

Organism
Desulfovibrio gigas
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi41 – 411Iron-sulfur 1 (4Fe-4S)
Metal bindingi44 – 441Iron-sulfur 1 (4Fe-4S)
Metal bindingi136 – 1361Iron-sulfur 1 (4Fe-4S)
Metal bindingi172 – 1721Iron-sulfur 1 (4Fe-4S)
Metal bindingi209 – 2091Iron-sulfur 2 (4Fe-4S); via pros nitrogen
Metal bindingi212 – 2121Iron-sulfur 2 (4Fe-4S)
Metal bindingi237 – 2371Iron-sulfur 2 (4Fe-4S)
Metal bindingi243 – 2431Iron-sulfur 2 (4Fe-4S)
Metal bindingi252 – 2521Iron-sulfur 3 (3Fe-4S)
Metal bindingi270 – 2701Iron-sulfur 3 (3Fe-4S)
Metal bindingi273 – 2731Iron-sulfur 3 (3Fe-4S)

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

3Fe-4S, 4Fe-4S, Iron, Iron-sulfur, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [NiFe] hydrogenase small subunit (EC:1.12.2.1)
Alternative name(s):
NiFe hydrogenlyase small chain
Gene namesi
Name:hydA
OrganismiDesulfovibrio gigas
Taxonomic identifieri879 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 23231 PublicationAdd
BLAST
Chaini24 – 288265Periplasmic [NiFe] hydrogenase small subunitPRO_0000013416Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Structurei

Secondary structure

1
288
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi32 – 376Combined sources
Helixi43 – 497Combined sources
Turni52 – 554Combined sources
Helixi56 – 627Combined sources
Beta strandi65 – 684Combined sources
Turni70 – 723Combined sources
Helixi78 – 8710Combined sources
Beta strandi90 – 10112Combined sources
Helixi103 – 1053Combined sources
Beta strandi109 – 1113Combined sources
Helixi116 – 1238Combined sources
Helixi124 – 1263Combined sources
Beta strandi127 – 1337Combined sources
Helixi134 – 1396Combined sources
Helixi142 – 1443Combined sources
Helixi155 – 1595Combined sources
Helixi160 – 1623Combined sources
Beta strandi167 – 1693Combined sources
Beta strandi171 – 1733Combined sources
Helixi176 – 18813Combined sources
Helixi201 – 2044Combined sources
Beta strandi205 – 2073Combined sources
Helixi209 – 2113Combined sources
Helixi215 – 2206Combined sources
Beta strandi225 – 2295Combined sources
Helixi230 – 2334Combined sources
Helixi239 – 2413Combined sources
Helixi245 – 2473Combined sources
Helixi252 – 2554Combined sources
Turni258 – 2603Combined sources
Turni263 – 2675Combined sources
Helixi278 – 2814Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85A/C25-288[»]
1YQ9X-ray2.35A/B25-288[»]
2FRVX-ray2.54A/C/E/G/I/S25-288[»]
ProteinModelPortaliP12943.
SMRiP12943. Positions 27-288.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12943.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.40.50.700. 1 hit.
4.10.480.10. 1 hit.
InterProiIPR027394. Cytochrome-c3_hydrogenase_C.
IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
[Graphical view]
PANTHERiPTHR30013. PTHR30013. 1 hit.
PfamiPF14720. NiFe_hyd_SSU_C. 1 hit.
PF01058. Oxidored_q6. 1 hit.
[Graphical view]
PIRSFiPIRSF000310. NiFe_hyd_ssu. 1 hit.
PRINTSiPR00614. NIHGNASESMLL.
TIGRFAMsiTIGR00391. hydA. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P12943-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFCTAVAVA MGMGPAFAPK VAEALTAKKR PSVVYLHNAE CTGCSESLLR
60 70 80 90 100
TVDPYVDELI LDVISMDYHE TLMAGAGHAV EEALHEAIKG DFVCVIEGGI
110 120 130 140 150
PMGDGGYWGK VGRRNMYDIC AEVAPKAKAV IAIGTCATYG GVQAAKPNPT
160 170 180 190 200
GTVGVNEALG KLGVKAINIA GCPPNPMNFV GTVVHLLTKG MPELDKQGRP
210 220 230 240 250
VMFFGETVHD NCPRLKHFEA GEFATSFGSP EAKKGYCLYE LGCKGPDTYN
260 270 280
NCPKQLFNQV NWPVQAGHPC IACSEPNFWD LYSPFYSA
Length:288
Mass (Da):30,816
Last modified:May 1, 1991 - v2
Checksum:i4827967DA110AE94
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti25 – 284LTAK → SEMQ AA sequence (PubMed:3322275).Curated
Sequence conflicti47 – 482SL → LV AA sequence (PubMed:3322275).Curated
Sequence conflicti48 – 481L → V in AAA23377 (PubMed:3322743).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18083 Genomic DNA. Translation: AAA23377.1. Sequence problems.
PIRiA32315. HQDVSG.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18083 Genomic DNA. Translation: AAA23377.1. Sequence problems.
PIRiA32315. HQDVSG.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85A/C25-288[»]
1YQ9X-ray2.35A/B25-288[»]
2FRVX-ray2.54A/C/E/G/I/S25-288[»]
ProteinModelPortaliP12943.
SMRiP12943. Positions 27-288.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP12943.

Family and domain databases

Gene3Di3.40.50.700. 1 hit.
4.10.480.10. 1 hit.
InterProiIPR027394. Cytochrome-c3_hydrogenase_C.
IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
[Graphical view]
PANTHERiPTHR30013. PTHR30013. 1 hit.
PfamiPF14720. NiFe_hyd_SSU_C. 1 hit.
PF01058. Oxidored_q6. 1 hit.
[Graphical view]
PIRSFiPIRSF000310. NiFe_hyd_ssu. 1 hit.
PRINTSiPR00614. NIHGNASESMLL.
TIGRFAMsiTIGR00391. hydA. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio gigas."
    Li C., Peck H.D. Jr., le Gall J., Przybyla A.E.
    DNA 6:539-551(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 24-69.
  2. "Analysis and comparison of nucleotide sequences encoding the genes for [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus."
    Voordouw G., Menon N.K., le Gall J., Choi E.S., Peck H.D. Jr., Przybyla A.E.
    J. Bacteriol. 171:2894-2899(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
  3. Cited for: PROTEIN SEQUENCE OF 25-58.
  4. "Isolation, amino acid analysis and N-terminal sequence determination of the two subunits of the nickel-containing hydrogenase of Desulfovibrio gigas."
    Niviere V., Forget N., Bovier-Lapierre G.E., Bonicel J., Hatchikian C.
    Biochimie 70:267-272(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 25-49.
  5. "Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas."
    Volbeda A., Charon M.-H., Piras C., Hatchikian E.C., Frey M., Fontecilla-Camps J.-C.
    Nature 373:580-587(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).

Entry informationi

Entry nameiPHNS_DESGI
AccessioniPrimary (citable) accession number: P12943
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: May 1, 1991
Last modified: October 14, 2015
This is version 112 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

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.