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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)DescriptionActionsGraphical viewLength
Metal bindingi67Iron-sulfur 1 (4Fe-4S)1
Metal bindingi70Iron-sulfur 1 (4Fe-4S)1
Metal bindingi164Iron-sulfur 1 (4Fe-4S)1
Metal bindingi200Iron-sulfur 1 (4Fe-4S)1
Metal bindingi238Iron-sulfur 2 (4Fe-4S); via pros nitrogen1
Metal bindingi241Iron-sulfur 2 (4Fe-4S)1
Metal bindingi266Iron-sulfur 2 (4Fe-4S)1
Metal bindingi272Iron-sulfur 2 (4Fe-4S)1
Metal bindingi281Iron-sulfur 3 (3Fe-4S)1
Metal bindingi299Iron-sulfur 3 (3Fe-4S)1
Metal bindingi302Iron-sulfur 3 (3Fe-4S)1

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
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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 50Tat-type signalAdd BLAST50
ChainiPRO_000001341951 – 317Periplasmic [NiFe] hydrogenase small subunitAdd BLAST267

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

1317
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi54 – 56Combined sources3
Beta strandi58 – 63Combined sources6
Helixi69 – 75Combined sources7
Turni78 – 81Combined sources4
Helixi82 – 87Combined sources6
Beta strandi91 – 94Combined sources4
Turni96 – 98Combined sources3
Helixi103 – 114Combined sources12
Beta strandi120 – 129Combined sources10
Helixi131 – 134Combined sources4
Beta strandi137 – 139Combined sources3
Helixi144 – 151Combined sources8
Helixi152 – 154Combined sources3
Beta strandi155 – 162Combined sources8
Helixi163 – 167Combined sources5
Helixi170 – 172Combined sources3
Helixi183 – 187Combined sources5
Helixi188 – 190Combined sources3
Beta strandi195 – 197Combined sources3
Beta strandi199 – 201Combined sources3
Helixi204 – 217Combined sources14
Helixi230 – 233Combined sources4
Beta strandi234 – 236Combined sources3
Helixi238 – 240Combined sources3
Helixi244 – 248Combined sources5
Beta strandi254 – 258Combined sources5
Helixi259 – 262Combined sources4
Helixi268 – 270Combined sources3
Helixi274 – 276Combined sources3
Helixi281 – 284Combined sources4
Turni287 – 289Combined sources3
Helixi293 – 295Combined sources3
Helixi307 – 310Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21853.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105E3S. Bacteria.
COG1740. LUCA.
HOGENOMiHOG000278822.
KOiK18008.
OMAiRSFNAHN.
OrthoDBiPOG091H05GB.

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
PDB 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.
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.
OrthoDBiPOG091H05GB.

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...

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: November 2, 2016
This is version 125 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.