Reviewed, UniProtKB/Swiss-Prot P12943 (PHNS_DESGI)

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

Organism

Desulfovibrio gigas

Taxonomic identifier

879 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	288 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 H(2) + 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.
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 Direct protein sequencing
Gene Ontology (GO)
Biological process	mitochondrial electron transport, NADH to ubiquinone Inferred from electronic annotation. Source: InterPro
Cellular component	ferredoxin hydrogenase complex Inferred from electronic annotation. Source: InterPro periplasmic space Inferred from electronic annotation. Source: UniProtKB-KW
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
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 23

23

Chain

24 – 288

265

Periplasmic [NiFe] hydrogenase small subunit

PRO_0000013416

Sites

Metal binding

41

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

44

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

136

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

172

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

209

1

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

Metal binding

212

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

237

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

243

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

252

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

270

1

Iron-sulfur 3 (3Fe-4S)

Metal binding

273

1

Iron-sulfur 3 (3Fe-4S)

Experimental info

Sequence conflict

25 – 28

4

LTAK → SEMQ AA sequence Ref.3

Sequence conflict

47 – 48

2

SL → LV AA sequence Ref.3

Sequence conflict

48

1

L → V in AAA23377. Ref.4

Secondary structure

1

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288

Helix Strand Turn

Details...

Beta strand

32 – 37

6

Helix

43 – 49

7

Turn

52 – 55

4

Helix

56 – 62

7

Beta strand

65 – 68

4

Turn

70 – 72

3

Helix

78 – 87

10

Beta strand

90 – 101

12

Helix

103 – 105

3

Beta strand

109 – 111

3

Helix

116 – 123

8

Helix

124 – 126

3

Beta strand

127 – 133

7

Helix

134 – 139

6

Helix

142 – 144

3

Helix

155 – 159

5

Helix

160 – 162

3

Beta strand

167 – 169

3

Beta strand

171 – 173

3

Helix

176 – 188

13

Helix

201 – 204

4

Beta strand

205 – 207

3

Helix

209 – 211

3

Helix

215 – 220

6

Helix

230 – 233

4

Helix

239 – 241

3

Helix

245 – 247

3

Helix

252 – 255

4

Turn

258 – 260

3

Turn

263 – 267

5

Helix

278 – 281

4

Sequences

	Sequence		Length	Mass (Da)
	P12943-1 [UniParc]. Last modified May 1, 1991. Version 2. Checksum: 4827967DA110AE94	FASTA	288	30,816
	10 20 30 40 50 60 MKFCTAVAVA MGMGPAFAPK VAEALTAKKR PSVVYLHNAE CTGCSESLLR TVDPYVDELI 70 80 90 100 110 120 LDVISMDYHE TLMAGAGHAV EEALHEAIKG DFVCVIEGGI PMGDGGYWGK VGRRNMYDIC 130 140 150 160 170 180 AEVAPKAKAV IAIGTCATYG GVQAAKPNPT GTVGVNEALG KLGVKAINIA GCPPNPMNFV 190 200 210 220 230 240 GTVVHLLTKG MPELDKQGRP VMFFGETVHD NCPRLKHFEA GEFATSFGSP EAKKGYCLYE 250 260 270 280 LGCKGPDTYN NCPKQLFNQV NWPVQAGHPC IACSEPNFWD LYSPFYSA

References

[1]	"Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio gigas." Li C., Peck H.D. Jr., le Gall J., Przybyla A.E. DNA 6:539-551(1987) [PubMed: 3322743] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 24-69.
[2]	"Analysis and comparison of nucleotide sequences encoding the genes for [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus." Voordouw G., Menon N.K., le Gall J., Choi E.S., Peck H.D. Jr., Przybyla A.E. J. Bacteriol. 171:2894-2899(1989) [PubMed: 2651421] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], 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: 3322275] [Abstract] Cited for: PROTEIN SEQUENCE OF 25-58.
[4]	"Isolation, amino acid analysis and N-terminal sequence determination of the two subunits of the nickel-containing hydrogenase of Desulfovibrio gigas." Niviere V., Forget N., Bovier-Lapierre G.E., Bonicel J., Hatchikian C. Biochimie 70:267-272(1988) [PubMed: 3134950] [Abstract] Cited for: PROTEIN SEQUENCE OF 25-49.
[5]	"Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas." Volbeda A., Charon M.-H., Piras C., Hatchikian E.C., Frey M., Fontecilla-Camps J.-C. Nature 373:580-587(1995) [PubMed: 7854413] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M18083 Genomic DNA. Translation: AAA23377.1. Sequence problems.

PIR

HQDVSG. A32315.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FRV	X-ray	2.85	A/C	25-288	[»]
1YQ9	X-ray	2.35	A/B	25-288	[»]
2FRV	X-ray	2.54	A/C/E/G/I/S	25-288	[»]

ModBase

Search...

Family and domain databases

InterPro

IPR001821. NiFe_hyd_ssu.
IPR013634. NiFe_hyd_ssu_N.
IPR006137. OxRdtase_q6.
[Graphical view]

Pfam

PF08425. NiFe_dehyd_N. 1 hit.
PF01058. Oxidored_q6. 1 hit.
[Graphical view]

PIRSF

PIRSF000310. NiFe_hyd_ssu. 1 hit.

PRINTS

PR00614. NIHGNASESMLL.

TIGRFAMs

TIGR00391. hydA. 1 hit.

ProtoNet

Search...

Other Resources

LinkHub

P12943.

Entry information

Entry name

PHNS_DESGI

Accession

Primary (citable) accession number: P12943

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	May 1, 1991
Last modified:	November 25, 2008
This is version 83 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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