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UniProtKB/Swiss-Prot entry P07598


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name PHFL_DESVH
Primary accession number P07598
Secondary accession numbers None
Integrated into Swiss-Prot on April 1, 1988
Sequence was last modified on April 1, 1988 (Sequence version 1)
Annotations were last modified on    November 25, 2008 (Entry version 86)
Name and origin of the protein
Protein name Periplasmic [Fe] hydrogenase large subunit
Synonyms EC 1.12.7.2
Fe hydrogenlyase
Gene name
Name: hydA
OrderedLocusNames: DVU_1769
From
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) [TaxID: 882] [HAMAP proteome]
Taxonomy Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3888621 [NCBI, ExPASy, EBI, Israel, Japan]
Voordouw G., Brenner S.;
"Nucleotide sequence of the gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough).";
Eur. J. Biochem. 148:515-520(1985).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1038/nbt959; PubMed=15077118 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.";
Nat. Biotechnol. 22:554-559(2004).
[3]
PROTEIN SEQUENCE OF 1-35.
DOI=10.1016/0006-291X(87)90376-7; PubMed=3322275 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"Identification of three classes of hydrogenase in the genus, Desulfovibrio.";
Biochem. Biophys. Res. Commun. 149:369-377(1987).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-15.
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.
[5]
MOSSBAUER SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
DOI=10.1021/ja003176+; PubMed=11456963 [NCBI, ExPASy, EBI, Israel, Japan]
Pereira A.S., Tavares P., Moura I., Moura J.J.G., Huynh B.H.;
"Mossbauer characterization of the iron-sulfur clusters in Desulfovibrio vulgaris hydrogenase.";
J. Am. Chem. Soc. 123:2771-2782(2001).
[6]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
DOI=10.1016/S0969-2126(99)80005-7; PubMed=10368269 [NCBI, ExPASy, EBI, Israel, Japan]
Nicolet Y., Piras C., Legrand P., Hatchikian E.C., Fontecilla-Camps J.-C.;
"Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.";
Structure 7:13-23(1999).
[7]
X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), ABSORPTION SPECTROSCOPY, EPR SPECTROSCOPY, AND FOURIER-TRANSFORM INFRARED SPECTROSCOPY.
DOI=10.1021/ja0020963; PubMed=11456758 [NCBI, ExPASy, EBI, Israel, Japan]
Nicolet Y., de Lacey A.L., Vernede X., Fernandez V.M., Hatchikian E.C., Fontecilla-Camps J.-C.;
"Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans.";
J. Am. Chem. Soc. 123:1596-1601(2001).
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.
  • COFACTOR: Binds 2 iron ions per subunit.
  • SUBUNIT: 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.
  • SIMILARITY: Contains 2 4Fe-4S ferredoxin-type domains.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
X02416; CAA26266.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AE017285; AAS96246.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
Z15142; CAA78848.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR A24551; HQDVFL.
RefSeq YP_010987.1; -.
3D structure databases
PDB
1E08; NMR; -; A=27-397.[ExPASy / RCSB / EBI]
1GX7; NMR; -; A=27-397.[ExPASy / RCSB / EBI]
1HFE; X-ray; 1.60 A; L/M=1-421.[ExPASy / RCSB / EBI]
Detailed list of linked structures.
PDBsum 1E08; -.
1GX7; -.
1HFE; -.
DisProt DP00108; -.
ModBase P07598.
Protein-protein interaction databases
DIP DIP:6186N; -.
Enzyme and pathway databases
BioCyc DVUL882:DVU_1769-MON; -.
Ontologies
GO
GO:0042597; Cellular component: periplasmic space (inferred from electronic annotation from UniProtKB-KW).
GO:0051539; Molecular function: 4 iron, 4 sulfur cluster binding (inferred from electronic annotation from UniProtKB-KW).
GO:0009055; Molecular function: electron carrier activity (inferred from electronic annotation from InterPro).
GO:0008901; Molecular function: ferredoxin hydrogenase activity (inferred from electronic annotation from InterPro).
GO:0005506; Molecular function: iron ion binding (inferred from electronic annotation from InterPro).
GO:0022900; Biological process: electron transport chain (inferred from electronic annotation from UniProtKB-KW).
GO:0006810; Biological process: transport (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR001450; 4Fe4S_Fe_S_bd.
IPR004108; Fe_hydrogenase_lsu_C.
IPR013352; Fe_hydrogenase_subset.
Graphical view of domain structure.
Pfam PF02906; Fe_hyd_lg_C; 1.
PF00037; Fer4; 2.
Pfam graphical view of domain structure.
PRINTS PR00353; 4FE4SFRDOXIN.
TIGRFAMs TIGR02512; Fe_only_hydrog; 1.
PROSITE PS00198; 4FE4S_FER_1; 2.
PS51379; 4FE4S_FER_2; 2.
PROSITE graphical view of domain structure (profiles).
Genome annotation databases
GeneID 2795816; -.
GenomeReviews AE017285_GR; DVU_1769.
KEGG dvu:DVU1769; -.
TIGR DVU_1769; -.
Phylogenomic databases
HOGENOM P07598; -.
Other
LinkHub P07598; -.
ProtoNet P07598.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; 4Fe-4S; Complete proteome; Direct protein sequencing; Electron transport; Iron; Iron-sulfur; Metal-binding; Oxidoreductase; Periplasm; Repeat; Transport.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   421  421     Periplasmic [Fe] hydrogenase large subunit. PRO_0000159239
DOMAIN   26    57  32     4Fe-4S ferredoxin-type 1. 
DOMAIN   59    86  28     4Fe-4S ferredoxin-type 2. 
METAL   35    35        Iron-sulfur 1 (4Fe-4S). 
METAL   38    38        Iron-sulfur 1 (4Fe-4S). 
METAL   41    41        Iron-sulfur 1 (4Fe-4S). 
METAL   45    45        Iron-sulfur 2 (4Fe-4S). 
METAL   66    66        Iron-sulfur 2 (4Fe-4S). 
METAL   69    69        Iron-sulfur 2 (4Fe-4S). 
METAL   72    72        Iron-sulfur 2 (4Fe-4S). 
METAL   76    76        Iron-sulfur 1 (4Fe-4S). 
METAL   179   179        Iron-sulfur 3 (4Fe-4S). 
METAL   234   234        Iron-sulfur 3 (4Fe-4S). 
METAL   378   378        Iron-sulfur 3 (4Fe-4S). 
METAL   382   382        Diiron subcluster. 
METAL   382   382        Iron-sulfur 3 (4Fe-4S). 
CONFLICT   35    35        C -> K (in Ref. 3; AA sequence). 
STRAND   4     6  3      
STRAND   9    11  3      
HELIX   22    24  3      
STRAND   27    30  4      
TURN   32    34  3      
HELIX   40    44  5      
HELIX   63    65  3      
HELIX   73    75  3      
STRAND   81    84  4      
HELIX   88    96  9      
STRAND   101   106  6      
HELIX   108   112  5      
HELIX   114   118  5      
HELIX   127   137  11      
STRAND   140   142  3      
HELIX   145   164  20      
STRAND   172   175  4      
HELIX   180   189  10      
HELIX   191   196  6      
HELIX   203   211  9      
HELIX   214   219  6      
HELIX   223   225  3      
STRAND   226   233  8      
HELIX   236   241  6      
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      
STRAND   332   340  9      
STRAND   343   352  10      
HELIX   353   355  3      
HELIX   356   364  9      
STRAND   371   378  8      
HELIX   382   384  3      
Sequence information
Length: 421 AA [This is the length of the unprocessed precursor] Molecular weight: 45951 Da [This is the MW of the unprocessed precursor] CRC64: 8E70A0775B68AACD [This is a checksum on the sequence]
        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 

P07598 in FASTA format

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