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Reviewed, UniProtKB/Swiss-Prot P12944 (PHNL_DESGI)

Last modified November 25, 2008. Version 75. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Periplasmic [NiFe] hydrogenase large subunit
    EC=1.12.2.1
Alternative name(s):
    NiFe hydrogenlyase large chain
Gene names
Name: hydB
OrganismDesulfovibrio gigas
Taxonomic identifier879 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

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Protein attributes

Sequence length551 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Catalytic activity

2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.

Cofactor

Binds 1 nickel ion per subunit.

Subunit structure

Heterodimer of a large and a small subunit.

Subcellular location

Periplasm.

Miscellaneous

Perhaps the leader of the small subunit serves as a transport vehicle for both subunits.

Sequence similarities

Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit family.

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Ontologies

Keywords

   Cellular componentPeriplasm
   LigandMetal-binding
Nickel
   Molecular functionOxidoreductase
   Technical term3D-structure
Direct protein sequencing

Gene Ontology (GO)

   Biological processoxidation reduction

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentperiplasmic space

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular functioncytochrome-c3 hydrogenase activity

Inferred from electronic annotation. Source: EC

ferredoxin hydrogenase activity

Inferred from electronic annotation. Source: InterPro

nickel ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 536535Periplasmic [NiFe] hydrogenase large subunit
PRO_0000013403
Propeptide537 – 55115
PRO_0000013404

Sites

Metal binding651Nickel
Metal binding681Nickel
Metal binding5301Nickel
Metal binding5331Nickel

Secondary structure

1 ................................................................................... 551
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P12944-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 4CF99AD3F75189B0

FASTA55161,480
        10         20         30         40         50         60 
MSEMQGNKIV VDPITRIEGH LRIEVEVEGG KIKNAWSMST LFRGLEMILK GRDPRDAQHF 

        70         80         90        100        110        120 
TQRACGVCTY VHALASVRAV DNCVGVKIPE NATLMRNLTM GAQYMHDHLV HFYHLHALDW 

       130        140        150        160        170        180 
VNVANALNAD PAKAARLAND LSPRKTTTES LKAVQAKVKA LVESGQLGIF TNAYFLGGHP 

       190        200        210        220        230        240 
AYVLPAEVDL IATAHYLEAL RVQVKAARAM AIFGAKNPHT QFTVVGGCTN YDSLRPERIA 

       250        260        270        280        290        300 
EFRKLYKEVR EFIEQVYITD LLAVAGFYKN WAGIGKTSNF LTCGEFPTDE YDLNSRYTPQ 

       310        320        330        340        350        360 
GVIWGNDLSK VDDFNPDLIE EHVKYSWYEG ADAHHPYKGV TKPKWTEFHG EDRYSWMKAP 

       370        380        390        400        410        420 
RYKGEAFEVG PLASVLVAYA KKHEPTVKAV DLVLKTLGVG PEALFSTLGR TAARGIQCLT 

       430        440        450        460        470        480 
AAQEVEVWLD KLEANVKAGK DDLYTDWQYP TESQGVGFVN APRGMLSHWI VQRGGKIENF 

       490        500        510        520        530        540 
QHVVPSTWNL GPRCAERKLS AVEQALIGTP IADPKRPVEI LRTVHSYDPC IACGVHVIDP 

       550 
ESNQVHKFRI L

« Hide

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References

[1]"Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio gigas."
Li C., Peck H.D. Jr., le Gall J., Przybyla A.E.
DNA 6:539-551(1987) [PubMed: 3322743] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-31.
[2]"Analysis and comparison of nucleotide sequences encoding the genes for [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus."
Voordouw G., Menon N.K., le Gall J., Choi E.S., Peck H.D. Jr., Przybyla A.E.
J. Bacteriol. 171:2894-2899(1989) [PubMed: 2651421] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
[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 2-30.
[4]"Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas."
Volbeda A., Charon M.-H., Piras C., Hatchikian E.C., Frey M., Fontecilla-Camps J.-C.
Nature 373:580-587(1995) [PubMed: 7854413] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).
+Additional computationally mapped references.

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Cross-references

Sequence databases

M18083 Genomic DNA. Translation: AAA23378.1. Sequence problems.
PIRHQDVLG. B32315.

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85B/D1-536[»]
1YQ9X-ray2.35H/I1-536[»]
2FRVX-ray2.54B/D/F/H/J/L1-536[»]
ModBaseSearch...

Family and domain databases

InterProIPR001501. Ni-dep_hyd_lsu.
[Graphical view]
PfamPF00374. NiFeSe_Hases. 1 hit.
[Graphical view]
PROSITEPS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

LinkHubP12944.

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Entry information

Entry namePHNL_DESGI
AccessionPrimary (citable) accession number: P12944
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: November 25, 2008
This is version 75 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents