Reviewed, UniProtKB/Swiss-Prot P21853 (PHNS_DESVM)

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:	DvMF_0271

Organism

Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [Complete proteome] [HAMAP]

Taxonomic identifier

883 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	317 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)

Function	Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.
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	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
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 iron 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 – 50

50

Tat-type signal

Chain

51 – 317

267

Periplasmic [NiFe] hydrogenase small subunit

PRO_0000013419

Sites

Metal binding

67

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

70

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

164

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

200

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

238

1

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

Metal binding

241

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

266

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

272

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

281

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

299

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

302

1

Iron-sulfur 3 (3Fe-4S)

Secondary structure

1

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317

Helix Strand Turn

Details...

Beta strand

54 – 56

3

Beta strand

58 – 65

8

Helix

69 – 75

7

Turn

78 – 81

4

Helix

82 – 87

6

Beta strand

91 – 94

4

Turn

96 – 98

3

Helix

103 – 115

13

Beta strand

121 – 129

9

Helix

132 – 134

3

Beta strand

137 – 139

3

Helix

144 – 151

8

Helix

152 – 154

3

Beta strand

155 – 162

8

Helix

163 – 167

5

Helix

170 – 172

3

Helix

183 – 186

4

Helix

188 – 190

3

Beta strand

195 – 197

3

Beta strand

199 – 201

3

Helix

204 – 217

14

Helix

230 – 233

4

Beta strand

234 – 236

3

Helix

238 – 240

3

Helix

244 – 248

5

Helix

259 – 262

4

Helix

268 – 270

3

Helix

274 – 276

3

Helix

281 – 284

4

Turn

287 – 289

3

Helix

292 – 295

4

Helix

307 – 310

4

Sequences

	Sequence		Length	Mass (Da)
	P21853-1 [UniParc]. Last modified May 1, 1991. Version 1. Checksum: 2EAF2D471932C8A8	FASTA	317	34,113
	10 20 30 40 50 60 MKISIGLGKE GVEERLAERG VSRRDFLKFC TAIAVTMGMG PAFAPEVARA LMGPRRPSVV 70 80 90 100 110 120 YLHNAECTGC SESVLRAFEP YIDTLILDTL SLDYHETIMA AAGDAAEAAL EQAVNSPHGF 130 140 150 160 170 180 IAVVEGGIPT AANGIYGKVA NHTMLDICSR ILPKAQAVIA YGTCATFGGV QAAKPNPTGA 190 200 210 220 230 240 KGVNDALKHL GVKAINIAGC PPNPYNLVGT IVYYLKNKAA PELDSLNRPT MFFGQTVHEQ 250 260 270 280 290 300 CPRLPHFDAG EFAPSFESEE ARKGWCLYEL GCKGPVTMNN CPKIKFNQTN WPVDAGHPCI 310 GCSEPDFWDA MTPFYQN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 2269874] [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].
[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: 9438867] [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: 10378274] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M58339 Genomic DNA. Translation: AAA23369.1.
CP001197 Genomic DNA. Translation: ACL07228.1.

PIR

A45865.

RefSeq

YP_002434696.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H2A	X-ray	1.80	S	1-317	[»]
1H2R	X-ray	1.40	S	51-317	[»]
1UBH	X-ray	1.35	S	51-317	[»]
1UBJ	X-ray	1.35	S	51-317	[»]
1UBK	X-ray	1.18	S	51-317	[»]
1UBL	X-ray	1.20	S	51-317	[»]
1UBM	X-ray	1.40	S	51-317	[»]
1UBO	X-ray	1.35	S	51-317	[»]
1UBR	X-ray	1.34	S	51-317	[»]
1UBT	X-ray	1.34	S	51-317	[»]
1UBU	X-ray	1.35	S	51-317	[»]
1WUH	X-ray	1.24	S	51-317	[»]
1WUI	X-ray	1.04	S	51-317	[»]
1WUJ	X-ray	1.40	S	51-317	[»]
1WUK	X-ray	1.10	S	51-317	[»]
1WUL	X-ray	1.50	S	51-317	[»]

ModBase

Search...

Genome annotation databases

GeneID

7172153.

GenomeReviews

Gene locus DvMF_0271 in contig CP001197_GR.

Organism-specific databases

CMR

Search...

Family and domain databases

InterPro

IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
IPR006311. Tat.
IPR017909. Twin_arg_translocation_Tat.
[Graphical view]

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_DESVM

Accession

Primary (citable) accession number: P21853
Secondary accession number(s): B8DPE1

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	May 1, 1991
Last modified:	June 16, 2009
This is version 75 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)