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Protein

Periplasmic [NiFe] hydrogenase small subunit

Gene

hydA

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi67 – 671Iron-sulfur 1 (4Fe-4S)
Metal bindingi70 – 701Iron-sulfur 1 (4Fe-4S)
Metal bindingi164 – 1641Iron-sulfur 1 (4Fe-4S)
Metal bindingi200 – 2001Iron-sulfur 1 (4Fe-4S)
Metal bindingi238 – 2381Iron-sulfur 2 (4Fe-4S); via pros nitrogen
Metal bindingi241 – 2411Iron-sulfur 2 (4Fe-4S)
Metal bindingi266 – 2661Iron-sulfur 2 (4Fe-4S)
Metal bindingi272 – 2721Iron-sulfur 2 (4Fe-4S)
Metal bindingi281 – 2811Iron-sulfur 3 (3Fe-4S)
Metal bindingi299 – 2991Iron-sulfur 3 (3Fe-4S)
Metal bindingi302 – 3021Iron-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

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-286-MONOMER.

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
Ordered Locus Names:DvMF_0271
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000001361 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 5050Tat-type signalAdd
BLAST
Chaini51 – 317267Periplasmic [NiFe] hydrogenase small subunitPRO_0000013419Add
BLAST

Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-41377N.
MINTiMINT-247646.
STRINGi883.DvMF_0271.

Structurei

Secondary structure

1
317
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi54 – 563Combined sources
Beta strandi58 – 636Combined sources
Helixi69 – 757Combined sources
Turni78 – 814Combined sources
Helixi82 – 876Combined sources
Beta strandi91 – 944Combined sources
Turni96 – 983Combined sources
Helixi103 – 11412Combined sources
Beta strandi120 – 12910Combined sources
Helixi131 – 1344Combined sources
Beta strandi137 – 1393Combined sources
Helixi144 – 1518Combined sources
Helixi152 – 1543Combined sources
Beta strandi155 – 1628Combined sources
Helixi163 – 1675Combined sources
Helixi170 – 1723Combined sources
Helixi183 – 1875Combined sources
Helixi188 – 1903Combined sources
Beta strandi195 – 1973Combined sources
Beta strandi199 – 2013Combined sources
Helixi204 – 21714Combined sources
Helixi230 – 2334Combined sources
Beta strandi234 – 2363Combined sources
Helixi238 – 2403Combined sources
Helixi244 – 2485Combined sources
Beta strandi254 – 2585Combined sources
Helixi259 – 2624Combined sources
Helixi268 – 2703Combined sources
Helixi274 – 2763Combined sources
Helixi281 – 2844Combined sources
Turni287 – 2893Combined sources
Helixi293 – 2953Combined sources
Helixi307 – 3104Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1H2AX-ray1.80S1-317[»]
1H2RX-ray1.40S51-317[»]
1UBHX-ray1.35S51-317[»]
1UBJX-ray1.35S51-317[»]
1UBKX-ray1.18S51-317[»]
1UBLX-ray1.20S51-317[»]
1UBMX-ray1.40S51-317[»]
1UBOX-ray1.35S51-317[»]
1UBRX-ray1.34S51-317[»]
1UBTX-ray1.34S51-317[»]
1UBUX-ray1.35S51-317[»]
1WUHX-ray1.24S51-317[»]
1WUIX-ray1.04S51-317[»]
1WUJX-ray1.40S51-317[»]
1WUKX-ray1.10S51-317[»]
1WULX-ray1.50S51-317[»]
4U9HX-ray0.89S53-317[»]
4U9IX-ray1.06S53-317[»]
ProteinModelPortaliP21853.
SMRiP21853. Positions 51-317.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21853.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105E3S. Bacteria.
COG1740. LUCA.
HOGENOMiHOG000278822.
KOiK18008.
OMAiRSFNAHN.
OrthoDBiEOG6J74S9.

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.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[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.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P21853-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKISIGLGKE GVEERLAERG VSRRDFLKFC TAIAVTMGMG PAFAPEVARA
60 70 80 90 100
LMGPRRPSVV YLHNAECTGC SESVLRAFEP YIDTLILDTL SLDYHETIMA
110 120 130 140 150
AAGDAAEAAL EQAVNSPHGF IAVVEGGIPT AANGIYGKVA NHTMLDICSR
160 170 180 190 200
ILPKAQAVIA YGTCATFGGV QAAKPNPTGA KGVNDALKHL GVKAINIAGC
210 220 230 240 250
PPNPYNLVGT IVYYLKNKAA PELDSLNRPT MFFGQTVHEQ CPRLPHFDAG
260 270 280 290 300
EFAPSFESEE ARKGWCLYEL GCKGPVTMNN CPKIKFNQTN WPVDAGHPCI
310
GCSEPDFWDA MTPFYQN
Length:317
Mass (Da):34,113
Last modified:May 1, 1991 - v1
Checksum:i2EAF2D471932C8A8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58339 Genomic DNA. Translation: AAA23369.1.
CP001197 Genomic DNA. Translation: ACL07228.1.
PIRiA45865.
RefSeqiWP_012611422.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL07228; ACL07228; DvMF_0271.
KEGGidvm:DvMF_0271.
PATRICi21770455. VBIDesVul86729_0282.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58339 Genomic DNA. Translation: AAA23369.1.
CP001197 Genomic DNA. Translation: ACL07228.1.
PIRiA45865.
RefSeqiWP_012611422.1. NC_011769.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1H2AX-ray1.80S1-317[»]
1H2RX-ray1.40S51-317[»]
1UBHX-ray1.35S51-317[»]
1UBJX-ray1.35S51-317[»]
1UBKX-ray1.18S51-317[»]
1UBLX-ray1.20S51-317[»]
1UBMX-ray1.40S51-317[»]
1UBOX-ray1.35S51-317[»]
1UBRX-ray1.34S51-317[»]
1UBTX-ray1.34S51-317[»]
1UBUX-ray1.35S51-317[»]
1WUHX-ray1.24S51-317[»]
1WUIX-ray1.04S51-317[»]
1WUJX-ray1.40S51-317[»]
1WUKX-ray1.10S51-317[»]
1WULX-ray1.50S51-317[»]
4U9HX-ray0.89S53-317[»]
4U9IX-ray1.06S53-317[»]
ProteinModelPortaliP21853.
SMRiP21853. Positions 51-317.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-41377N.
MINTiMINT-247646.
STRINGi883.DvMF_0271.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL07228; ACL07228; DvMF_0271.
KEGGidvm:DvMF_0271.
PATRICi21770455. VBIDesVul86729_0282.

Phylogenomic databases

eggNOGiENOG4105E3S. Bacteria.
COG1740. LUCA.
HOGENOMiHOG000278822.
KOiK18008.
OMAiRSFNAHN.
OrthoDBiEOG6J74S9.

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-286-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP21853.

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.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[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.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F."
    Deckers H.M., Wilson F.R., Voordouw G.
    J. Gen. Microbiol. 136:2021-2028(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
    Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Miyazaki F / DSM 19637.
  3. "Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis."
    Higuchi Y., Yagi T., Yasuoka N.
    Structure 5:1671-1680(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
  4. "Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution."
    Higuchi Y., Ogata H., Miki K., Yasuoka N., Yagi T.
    Structure 7:549-556(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).

Entry informationi

Entry nameiPHNS_DESVM
AccessioniPrimary (citable) accession number: P21853
Secondary accession number(s): B8DPE1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: May 1, 1991
Last modified: July 6, 2016
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

Keywords - Technical termi

3D-structure, Complete proteome, 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.