P07603 (PHFS_DESVH) Reviewed, UniProtKB/Swiss-Prot

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) [Reference proteome] [HAMAP]

Taxonomic identifier

882 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio › Desulfovibrio vulgaris

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 Reference proteome
Gene Ontology (GO)
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: InterPro 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

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.

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.

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 [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
[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 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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

PIR

HQDVFS. B24551.

RefSeq

YP_010988.1. NC_002937.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P07603.

SMR

P07603. Positions 36-123.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6187N.

STRING

882.DVU1770.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAS96247; AAS96247; DVU_1770.

GeneID

2795817.

KEGG

dvu:DVU1770.

PATRIC

32063306. VBIDesVul119526_1626.

Phylogenomic databases

eggNOG

NOG282997.

KO

K00534.

OMA

RVSHANP.

ProtClustDB

CLSK907410.

Enzyme and pathway databases

BioCyc

DVUL882:GJIL-1811-MONOMER.

Family and domain databases

Gene3D

4.10.260.20. 1 hit.

InterPro

IPR008953. Fe_hydrogenase_ssu.
IPR003149. Fe_hydrogenase_ssu-like.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view]

Pfam

PF02256. Fe_hyd_SSU. 1 hit.
[Graphical view]

SMART

SM00902. Fe_hyd_SSU. 1 hit.
[Graphical view]

SUPFAM

SSF48674. Fe_hydrog_small. 1 hit.

TIGRFAMs

TIGR01409. TAT_signal_seq. 1 hit.

PROSITE

PS51318. TAT. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P07603.

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:	May 1, 2013
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program