P13063 (PHSS_DESBA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Periplasmic [NiFeSe] hydrogenase small subunit EC=1.12.99.6 Alternative name(s): NiFeSe hydrogenlyase small chain
Organism	Desulfovibrio baculatus (Desulfomicrobium baculatus)
Taxonomic identifier	899 [NCBI]
Taxonomic lineage	cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Deltaproteobacteria › Desulfovibrionales › Desulfomicrobiaceae › Desulfomicrobium

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	H2 + A = AH2.
Cofactor	Binds 3 4Fe-4S clusters. Cluster 1 is referred to as proximal, cluster 2 as distal, cluster 3 as medial.
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	4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure 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	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW NADH dehydrogenase (ubiquinone) activity Inferred from electronic annotation. Source: InterPro ferredoxin hydrogenase activity Inferred from electronic annotation. Source: InterPro hydrogenase (acceptor) activity Inferred from electronic annotation. Source: EC 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 – 32

32

Tat-type signal Ref.3

Chain

33 – 315

283

Periplasmic [NiFeSe] hydrogenase small subunit

PRO_0000013420

Sites

Metal binding

50

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

53

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

158

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

196

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

240

1

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

Metal binding

243

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

263

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

269

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

278

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

290

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

296

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

299

1

Iron-sulfur 3 (4Fe-4S)

Secondary structure

1

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315

Helix Strand Turn

Details...

Beta strand

40 – 48

9

Helix

52 – 58

7

Turn

61 – 64

4

Helix

65 – 71

7

Beta strand

73 – 77

5

Turn

79 – 81

3

Helix

86 – 99

14

Turn

100 – 102

3

Beta strand

103 – 113

11

Helix

115 – 118

4

Beta strand

121 – 124

4

Beta strand

131 – 133

3

Helix

138 – 145

8

Helix

146 – 148

3

Beta strand

149 – 156

8

Helix

157 – 161

5

Helix

164 – 166

3

Helix

177 – 184

8

Beta strand

190 – 193

4

Helix

200 – 215

16

Turn

217 – 219

3

Helix

232 – 235

4

Beta strand

236 – 238

3

Turn

239 – 242

4

Helix

246 – 250

5

Beta strand

260 – 264

5

Helix

265 – 267

3

Helix

271 – 273

3

Helix

278 – 281

4

Turn

284 – 287

4

Helix

290 – 293

4

Turn

302 – 305

4

Helix

306 – 308

3

Sequences

	Sequence		Length	Mass (Da)
	P13063 [UniParc]. Last modified January 1, 1990. Version 1. Checksum: A3C592F12B95ED83	FASTA	315	34,221
	10 20 30 40 50 60 MSLSRREFVK LCSAGVAGLG ISQIYHPGIV HAMTEGAKKA PVIWVQGQGC TGCSVSLLNA 70 80 90 100 110 120 VHPRIKEILL DVISLEFHPT VMASEGEMAL AHMYEIAEKF NGNFFLLVEG AIPTAKEGRY 130 140 150 160 170 180 CIVGETLDAK GHHHEVTMME LIRDLAPKSL ATVAVGTCSA YGGIPAAEGN VTGSKSVRDF 190 200 210 220 230 240 FADEKIEKLL VNVPGCPPHP DWMVGTLVAA WSHVLNPTEH PLPELDDDGR PLLFFGDNIH 250 260 270 280 290 300 ENCPYLDKYD NSEFAETFTK PGCKAELGCK GPSTYADCAK RRWNNGINWC VENAVCIGCV 310 EPDFPDGKSP FYVAE

References

[1]	"Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus." Menon N.K., Peck H.D. Jr., le Gall J., Przybyla A.E. J. Bacteriol. 169:5401-5407(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Erratum Menon N.K., Pect H.D. Jr., le Gall J., Przybyla A.E. J. Bacteriol. 170:4429-4429(1988) Cited for: SEQUENCE REVISION.
[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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 33-67. Strain: DSM 1743.
[4]	"The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center." Garcin E., Vernede X., Hatchikian E.C., Volbeda A., Frey M., Fontecilla-Camps J.-C. Structure 7:557-566(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M18271 Genomic DNA. Translation: AAA23376.1.

PIR

HQDVSB. A28380.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CC1	X-ray	2.15	S	33-315	[»]

ProteinModelPortal

P13063.

SMR

P13063. Positions 38-315.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6126N.

MINT

MINT-96877.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.50.700. 1 hit.
4.10.480.10. 1 hit.

InterPro

IPR027394. Cytochrome-c3_hydrogenase_C.
IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[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...

Other

EvolutionaryTrace

P13063.

Entry information

Entry name

PHSS_DESBA

Accession

Primary (citable) accession number: P13063

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	May 29, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program