Periplasmic [NiFe] hydrogenase small subunit precursor - Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)

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P13061 (PHNS_DESDA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 86. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Periplasmic [NiFe] hydrogenase small subunit
EC=1.12.2.1

Alternative name(s):
NiFe hydrogenlyase small chain

Gene names

Name:	hydA
Ordered Locus Names:	Ddes_1039

Organism

Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949) [Complete proteome] [HAMAP]

Taxonomic identifier

525146 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	315 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	2 H₂ + ferricytochrome c3 = 4 H⁺ + ferrocytochrome c3.
Cofactor	Binds 2 4Fe-4S clusters. Binds 1 3Fe-4S cluster.
Subunit structure	Heterodimer of a large and a small subunit.
Subcellular location	Periplasm.
Post-translational modification	Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.
Sequence similarities	Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit family.

Ontologies

Keywords
Cellular component	Periplasm
Domain	Signal
Ligand	3Fe-4S 4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Cellular component	ferredoxin hydrogenase complex Inferred from electronic annotation. Source: InterPro periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW NADH dehydrogenase (ubiquinone) activity Inferred from electronic annotation. Source: InterPro cytochrome-c3 hydrogenase activity Inferred from electronic annotation. Source: EC ferredoxin hydrogenase activity Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW quinone binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 49

Tat-type signal Ref.2 Ref.3

Chain

50 – 315

266

Periplasmic [NiFe] hydrogenase small subunit

PRO_0000204353

Sites

Metal binding

Iron-sulfur 1 (4Fe-4S) By similarity

Metal binding

Iron-sulfur 1 (4Fe-4S) By similarity

Metal binding

163

Iron-sulfur 1 (4Fe-4S) By similarity

Metal binding

199

Iron-sulfur 1 (4Fe-4S) By similarity

Metal binding

236

Iron-sulfur 2 (4Fe-4S); via pros nitrogen By similarity

Metal binding

239

Iron-sulfur 2 (4Fe-4S) By similarity

Metal binding

264

Iron-sulfur 2 (4Fe-4S) By similarity

Metal binding

270

Iron-sulfur 2 (4Fe-4S) By similarity

Metal binding

279

Iron-sulfur 3 (3Fe-4S) By similarity

Metal binding

297

Iron-sulfur 3 (3Fe-4S) By similarity

Metal binding

300

Iron-sulfur 3 (3Fe-4S) By similarity

Experimental info

Sequence conflict

117

D → G AA sequence Ref.2

Sequence conflict

165

C → S AA sequence Ref.2

Sequence conflict

176

P → PNP AA sequence Ref.2

Sequence conflict

185

C → A AA sequence Ref.2

Sequence conflict

195 – 204

NVPGCPPNPL → VIAGCNPNTI AA sequence Ref.2

Sequence conflict

242

R → A AA sequence Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P13061 [UniParc].

Last modified May 5, 2009. Version 3.
Checksum: F19E84851D9EA766
Show »

FASTA

315

33,912

        10         20         30         40         50         60 
MRIAVGLGKE GGEERLERQG ISRRDFMKFC TAVAVAMGMG PAFATDVAAA LTGRRPSVVY 

        70         80         90        100        110        120 
LHAAECTGCS EALLRTYQPF IDTLILDTIS LDYHETIMAA AGEAAEEALQ AAVNGPDGFI 

       130        140        150        160        170        180 
CLVEGAIPTG MDNKYGYIAG HTMYDICKNI LPKAKAVVSI GTCACYGGIQ AAKPNPTAAK 

       190        200        210        220        230        240 
GINDCYADLG VKAINVPGCP PNPLNMVGTL VAFLKGQKIE LDEVGRPVMF FGQSVHDLCE 

       250        260        270        280        290        300 
RRKHFDAGEF APSFNSEEAR KGWCLYDVGC KGPETYNNCP KVLFNETNWP VAAGHPCIGC 

       310 
SEPNFWDDMT PFYQN

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete sequence of Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774." US DOE Joint Genome Institute Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Lu M., Kiss H., Meineke L., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L. , Kyrpides N., Ovchinnikova G., Hazen T.C. Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 27774 / DSM 6949.
[2]	"The primary structure of the beta subunit of Desulfovibrio desulfuricans (ATCC 27774) [NiFe] hydrogenase." Franco R., Calvete J.J., Thole H.H., Raida M., Moura I., Moura J.J.G. Protein Pept. Lett. 4:131-138(1997) Cited for: PROTEIN SEQUENCE OF 50-315, SEQUENCE REVISION TO 65 AND 67.
[3]	"Identification of three classes of hydrogenase in the genus, Desulfovibrio." Prickril B.C., He S.H., Li C., Menon N.K., Choi E.S., Przybyla A.E., Dervartanian D.V., Peck H.D. Jr., Fauque G., le Gall J., Teixeira M., Moura I., Moura J.J.G., Patil D., Huynh B.H. Biochem. Biophys. Res. Commun. 149:369-377(1987) [PubMed: 3322275] [Abstract] Cited for: PROTEIN SEQUENCE OF 50-67.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001358 Genomic DNA. Translation: ACL48946.1.
PIR	F27480.
RefSeq	YP_002479624.1. NC_011883.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	P13061.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	7284720.
GenomeReviews	Gene locus Ddes_1039 in contig CP001358_GR.
KEGG	dds:Ddes_1039.
PATRIC	21735736. VBIDesDes50650_1230.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG575615.
ProtClustDB	CLSK705494.
Family and domain databases
InterPro	IPR006137. NADH_UbQ_OxRdtase-like_20kDa. IPR001821. NiFe_hydrogenase_ssu. IPR006311. TAT_signal. IPR019546. TAT_signal_bac_arc. [Graphical view]
Gene3D	G3DSA:3.40.50.700. G3DSA:3.40.50.700. 1 hit.
KO	K06282.
Pfam	PF01058. Oxidored_q6. 1 hit. [Graphical view]
PIRSF	PIRSF000310. NiFe_hyd_ssu. 1 hit.
PRINTS	PR00614. NIHGNASESMLL.
TIGRFAMs	TIGR00391. HydA. 1 hit. TIGR01409. TAT_signal_seq. 1 hit.
PROSITE	PS51318. TAT. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PHNS_DESDA

Accession

Primary (citable) accession number: P13061
Secondary accession number(s): B8IZL9

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	May 5, 2009
Last modified:	January 25, 2012
This is version 86 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents