Reviewed, UniProtKB/Swiss-Prot P07603 (PHFS_DESVH)

Names and origin

Protein names

Recommended name:
    Periplasmic [Fe] hydrogenase small subunit
    EC=1.12.7.2
Alternative name(s):
    Fe hydrogenlyase small chain

Gene names

Name:	hydB
Ordered Locus Names:	DVU_1770

Organism

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) [Complete proteome] [HAMAP]

Taxonomic identifier

882 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	123 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	May be involved in hydrogen uptake for the reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is likely to be the physiological electron carrier for the enzyme.
Catalytic activity	H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+.
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.

Ontologies

Keywords
Cellular component	Periplasm
Domain	Signal
Ligand	Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	electron carrier activity Inferred from electronic annotation. Source: InterPro ferredoxin hydrogenase activity Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW iron-sulfur cluster 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 – 34

34

Tat-type signal Ref.3

Chain

35 – 123

89

Periplasmic [Fe] hydrogenase small subunit

PRO_0000013413

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

123

Helix Strand Turn

Details...

Helix

39 – 56

18

Helix

62 – 64

3

Helix

66 – 74

9

Helix

82 – 88

7

Helix

97 – 104

8

Helix

113 – 116

4

Sequences

	Sequence		Length	Mass (Da)
	P07603-1 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: 2F4F7A4304ECD47B	FASTA	123	13,624
	10 20 30 40 50 60 MQIASITRRG FLKVACVTTG AALIGIRMTG KAVAAVKQIK DYMLDRINGV YGADAKFPVR 70 80 90 100 110 120 ASQDNTQVKA LYKSYLEKPL GHKSHDLLHT HWFDKSKGVK ELTTAGKLPN PRASEFEGPY PYE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough)." Voordouw G., Brenner S. Eur. J. Biochem. 148:515-520(1985) [PubMed: 3888621] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough." Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T., Kolonay J.F., Eisen J.A., Ward N.L., Methe B.A., Brinkac L.M., Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Fouts D.E. , Haft D.H., Selengut J., Peterson J.D., Davidsen T.M., Zafar N., Zhou L., Radune D., Dimitrov G., Hance M., Tran K., Khouri H.M., Gill J., Utterback T.R., Feldblyum T.V., Wall J.D., Voordouw G., Fraser C.M. Nat. Biotechnol. 22:554-559(2004) [PubMed: 15077118] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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 35-69.
[4]	"Putative signal peptide on the small subunit of the periplasmic hydrogenase from Desulfovibrio vulgaris." Prickril B.C., Czechowski M.H., Przybyla A.E., Peck H.D. Jr., le Gall J. J. Bacteriol. 167:722-725(1986) [PubMed: 3525521] [Abstract] Cited for: SIGNAL SEQUENCE CLEAVAGE SITE.
[5]	"Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center." Nicolet Y., Piras C., Legrand P., Hatchikian E.C., Fontecilla-Camps J.-C. Structure 7:13-23(1999) [PubMed: 10368269] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X02416 Genomic DNA. Translation: CAA26267.1.
AE017285 Genomic DNA. Translation: AAS96247.1.

PIR

HQDVFS. B24551.

RefSeq

YP_010988.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E08	NMR	-	D	36-123	[»]
1GX7	NMR	-	D	36-123	[»]
1HFE	X-ray	1.60	S/T	1-123	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:6187N.

Genome annotation databases

GeneID

2795817.

GenomeReviews

Gene locus DVU_1770 in contig AE017285_GR.

KEGG

dvu:DVU1770.

TIGR

DVU_1770.

Phylogenomic databases

HOGENOM

P07603.

OMA

P07603. VSHANPA.

Enzyme and pathway databases

BioCyc

DVUL882:DVU_1770-MON.

Family and domain databases

InterPro

IPR003149. Fe_hydrogenase_ssu-like.
IPR006311. Tat.
IPR017909. Twin_arg_translocation_Tat.
[Graphical view]

Gene3D

G3DSA:4.10.260.20. Fe_hyd_ssu-like. 1 hit.

Pfam

PF02256. Fe_hyd_SSU. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01409. TAT_signal_seq. 1 hit.

PROSITE

PS51318. TAT. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PHFS_DESVH

Accession

Primary (citable) accession number: P07603

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	June 16, 2009
This is version 81 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)