P07598 (PHFL_DESVH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Periplasmic [Fe] hydrogenase large subunit
EC=1.12.7.2

Alternative name(s):
Fe hydrogenlyase

Gene names

Name:	hydA
Ordered Locus Names:	DVU_1769

Organism

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)

Taxonomic identifier

882 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	421 AA.
Sequence status	Complete.
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+.
Cofactor	Binds 3 4Fe-4S clusters per subunit. Binds 2 iron ions per subunit.
Subunit structure	Heterodimer of a large and a small subunit.
Subcellular location	Periplasm.
Miscellaneous	[Fe], [NiFe], and [NiFeSe] hydrogenases appear to represent three distinct enzymes having hydrogenase activity.
Sequence similarities	Contains 2 4Fe-4S ferredoxin-type domains.

Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Periplasm
Domain	Repeat
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 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
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 421

421

Periplasmic [Fe] hydrogenase large subunit

PRO_0000159239

Regions

Domain

26 – 57

32

4Fe-4S ferredoxin-type 1

Domain

59 – 86

28

4Fe-4S ferredoxin-type 2

Sites

Metal binding

35

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

38

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

41

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

45

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

66

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

69

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

72

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

76

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

179

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

234

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

378

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

382

1

Diiron subcluster

Metal binding

382

1

Iron-sulfur 3 (4Fe-4S)

Experimental info

Sequence conflict

35

1

C → K AA sequence Ref.3

Secondary structure

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421

Helix Strand Turn

Details...

Beta strand

4 – 6

3

Beta strand

9 – 11

3

Helix

22 – 24

3

Beta strand

27 – 30

4

Turn

32 – 34

3

Helix

40 – 44

5

Helix

63 – 65

3

Helix

73 – 75

3

Beta strand

81 – 84

4

Helix

88 – 96

9

Beta strand

101 – 106

6

Helix

108 – 112

5

Helix

114 – 118

5

Helix

127 – 137

11

Beta strand

140 – 142

3

Helix

145 – 164

20

Beta strand

172 – 175

4

Helix

180 – 189

10

Helix

191 – 196

6

Helix

203 – 211

9

Helix

214 – 219

6

Helix

223 – 225

3

Beta strand

226 – 233

8

Helix

236 – 241

6

Beta strand

256 – 259

4

Helix

260 – 269

10

Helix

274 – 276

3

Turn

284 – 286

3

Helix

291 – 294

4

Helix

295 – 297

3

Helix

301 – 315

15

Helix

325 – 327

3

Beta strand

332 – 340

9

Beta strand

343 – 352

10

Helix

353 – 355

3

Helix

356 – 364

9

Beta strand

371 – 378

8

Helix

382 – 384

3

Sequences

	Sequence		Length	Mass (Da)
	P07598 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: 8E70A0775B68AACD	FASTA	421	45,951
	10 20 30 40 50 60 MSRTVMERIE YEMHTPDPKA DPDKLHFVQI DEAKCIGCDT CSQYCPTAAI FGEMGEPHSI 70 80 90 100 110 120 PHIEACINCG QCLTHCPENA IYEAQSWVPE VEKKLKDGKV KCIAMPAPAV RYALGDAFGM 130 140 150 160 170 180 PVGSVTTGKM LAALQKLGFA HCWDTEFTAD VTIWEEGSEF VERLTKKSDM PLPQFTSCCP 190 200 210 220 230 240 GWQKYAETYY PELLPHFSTC KSPIGMNGAL AKTYGAERMK YDPKQVYTVS IMPCIAKKYE 250 260 270 280 290 300 GLRPELKSSG MRDIDATLTT RELAYMIKKA GIDFAKLPDG KRDSLMGEST GGATIFGVTG 310 320 330 340 350 360 GVMEAALRFA YEAVTGKKPD SWDFKAVRGL DGIKEATVNV GGTDVKVAVV HGAKRFKQVC 370 380 390 400 410 420 DDVKAGKSPY HFIEYMACPG GCVCGGGQPV MPGVLEAMDR TTTRLYAGLK KRLAMASANK A

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]. 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: 3322275] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-35.
[4]	van den Berg W.A.M., Stokkermans J.P.W.G., van Dongen W.M.A.M. Submitted (SEP-1992) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-15.
[5]	"Mossbauer characterization of the iron-sulfur clusters in Desulfovibrio vulgaris hydrogenase." Pereira A.S., Tavares P., Moura I., Moura J.J.G., Huynh B.H. J. Am. Chem. Soc. 123:2771-2782(2001) [PubMed: 11456963] [Abstract] Cited for: MOSSBAUER SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
[6]	"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).
[7]	"Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans." Nicolet Y., de Lacey A.L., Vernede X., Fernandez V.M., Hatchikian E.C., Fontecilla-Camps J.-C. J. Am. Chem. Soc. 123:1596-1601(2001) [PubMed: 11456758] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), ABSORPTION SPECTROSCOPY, EPR SPECTROSCOPY, FOURIER-TRANSFORM INFRARED SPECTROSCOPY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02416 Genomic DNA. Translation: CAA26266.1.
AE017285 Genomic DNA. Translation: AAS96246.1.
Z15142 Genomic DNA. Translation: CAA78848.1.

PIR

HQDVFL. A24551.

RefSeq

YP_010987.1. NC_002937.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E08	NMR	-	A	27-397	[»]
1GX7	NMR	-	A	27-397	[»]
1HFE	X-ray	1.60	L/M	1-421	[»]

ProteinModelPortal

P07598.

SMR

P07598. Positions 2-397.

DisProt

DP00108.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6186N.

STRING

P07598.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

2795816.

GenomeReviews

Gene locus DVU_1769 in contig AE017285_GR.

KEGG

dvu:DVU1769.

PATRIC

32063304. VBIDesVul119526_1625.

TIGR

DVU_1769.

Phylogenomic databases

eggNOG

COG4624.

HOGENOM

HBG305296.

OMA

SAIEETH.

ProtClustDB

CLSK705400.

Enzyme and pathway databases

BioCyc

DVUL882:DVU_1769-MONOMER.

Family and domain databases

InterPro

IPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR009016. Fe_hydrogenase.
IPR004108. Fe_hydrogenase_lsu_C.
IPR013352. Fe_hydrogenase_subset.
[Graphical view]

KO

K00533.

Pfam

PF02906. Fe_hyd_lg_C. 1 hit.
PF00037. Fer4. 2 hits.
[Graphical view]

SUPFAM

SSF53920. Fe_hydrog. 1 hit.

TIGRFAMs

TIGR02512. Fe_only_hydrog. 1 hit.

PROSITE

PS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PHFL_DESVH

Accession

Primary (citable) accession number: P07598

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	January 25, 2012
This is version 107 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program