Reviewed, UniProtKB/Swiss-Prot P18187 (PHNS_DESFR)

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 fructosovorans

Taxonomic identifier

878 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	314 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	3D-structure Direct protein sequencing
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 – 49

49

Tat-type signal Ref.2

Chain

50 – 314

265

Periplasmic [NiFe] hydrogenase small subunit

PRO_0000013415

Sites

Metal binding

67

1

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

Metal binding

70

1

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

Metal binding

160

1

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

Metal binding

197

1

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

Metal binding

234

1

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

Metal binding

237

1

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

Metal binding

262

1

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

Metal binding

268

1

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

Metal binding

277

1

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

Metal binding

295

1

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

Metal binding

298

1

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

Secondary structure

1

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314

Helix Strand Turn

Details...

Beta strand

58 – 63

6

Helix

69 – 74

6

Turn

78 – 81

4

Helix

82 – 88

7

Beta strand

91 – 95

5

Turn

96 – 98

3

Helix

103 – 114

12

Beta strand

120 – 129

10

Helix

131 – 134

4

Beta strand

137 – 139

3

Helix

144 – 153

10

Beta strand

158 – 162

5

Helix

163 – 166

4

Helix

169 – 171

3

Helix

182 – 186

5

Beta strand

191 – 193

3

Beta strand

195 – 197

3

Helix

200 – 212

13

Helix

225 – 228

4

Beta strand

229 – 231

3

Helix

233 – 235

3

Helix

239 – 243

5

Helix

254 – 257

4

Helix

263 – 265

3

Helix

269 – 271

3

Helix

276 – 279

4

Turn

282 – 284

3

Turn

287 – 291

5

Helix

302 – 305

4

Sequences

	Sequence		Length	Mass (Da)
	P18187-1 [UniParc]. Last modified July 22, 2008. Version 4. Checksum: 48BE00FE51D23A68	FASTA	314	33,621
	10 20 30 40 50 60 MNFSVGLGRD DAEKRLVQNG VSRRDFMKFC ATVAAAMGMG PAFAPKVAEA LTAKHRPSVV 70 80 90 100 110 120 WLHNAECTGC TEAAIRTIKP YIDALILDTI SLDYQETIMA AAGEAAEAAL HQALEGKDGY 130 140 150 160 170 180 YLVVEGGLPT IDGGQWGMVA GHPMIETTKK AAAKAKGIIC IGTCSAYGGV QKAKPNPSQA 190 200 210 220 230 240 KGVSEALGVK TINIPGCPPN PINFVGAVVH VLTKGIPDLD ENGRPKLFYG ELVHDNCPRL 250 260 270 280 290 300 PHFEASEFAP SFDSEEAKKG FCLYELGCKG PVTYNNCPKV LFNQVNWPVQ AGHPCLGCSE 310 PDFWDTMTPF YEQG

References

[1]	"Cloning and sequencing of the locus encoding the large and small subunit genes of the periplasmic [NiFe]hydrogenase from Desulfovibrio fructosovorans." Rousset M., Dermoun Z., Matchikian C.E., Belaich J.-P. Gene 94:95-101(1990) [PubMed: 2227457] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 49200 / DSM 3604 / VKM B-1801 / JJ.
[2]	"Characterization of the nickel-iron periplasmic hydrogenase from Desulfovibrio fructosovorans." Hatchikian C.E., Traore A.S., Fernandez V.M., Cammack R. Eur. J. Biochem. 187:635-643(1990) [PubMed: 2154378] [Abstract] Cited for: PROTEIN SEQUENCE OF 50-60.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M35333 Genomic DNA. Translation: AAA23371.2.

PIR

S08198. JQ0761.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FRF	X-ray	2.70	S	51-314	[»]
1YQW	X-ray	1.83	A/B/C	51-313	[»]
1YRQ	X-ray	2.10	A/B/C/D/F/G	51-313	[»]
3CUR	X-ray	2.40	A/B/C	51-314	[»]
3CUS	X-ray	2.20	A/B/C	51-314	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:6172N.

Enzyme and pathway databases

BRENDA

1.12.2.1. 259091.

Family and domain databases

InterPro

IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
IPR006311. Tat.
IPR019546. TAT_signal.
IPR017909. Twin_arg_translocation_Tat.
[Graphical view]

Pfam

PF01058. Oxidored_q6. 1 hit.
PF10518. TAT_signal. 1 hit.
[Graphical view]

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_DESFR

Accession

Primary (citable) accession number: P18187

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	July 22, 2008
Last modified:	June 16, 2009
This is version 83 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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