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P21852 (PHNL_DESVM) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

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
Ordered Locus Names:DvMF_0270
OrganismDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [Complete proteome] [HAMAP]
Taxonomic identifier883 [NCBI]
Taxonomic lineageBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Protein attributes

Sequence length567 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.

Catalytic activity

2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.

Cofactor

Nickel.

Iron.

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.

Ontologies

Keywords
   Cellular componentPeriplasm
   LigandIron
Magnesium
Metal-binding
Nickel
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Cellular_componentperiplasmic space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncytochrome-c3 hydrogenase activity

Inferred from electronic annotation. Source: UniProtKB-EC

ferredoxin hydrogenase activity

Inferred from electronic annotation. Source: InterPro

nickel cation binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 552552Periplasmic [NiFe] hydrogenase large subunit
PRO_0000013405
Propeptide553 – 56715
PRO_0000013406

Sites

Metal binding621Magnesium
Metal binding811Nickel
Metal binding841Iron
Metal binding841Nickel
Metal binding4981Magnesium; via carbonyl oxygen
Metal binding5461Nickel
Metal binding5491Iron
Metal binding5491Nickel
Metal binding5521Magnesium; via tele nitrogen

Experimental info

Sequence conflict1801S → T in AAA23370. Ref.1
Sequence conflict514 – 5152KL → NV in AAA23370. Ref.1

Secondary structure

........................................................................................ 567
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P21852 [UniParc].

Last modified April 14, 2009. Version 2.
Checksum: 8BE92277C0E46FDA

FASTA56762,641
        10         20         30         40         50         60 
MSGCRAQNAP GGIPVTPKSS YSGPIVVDPV TRIEGHLRIE VEVENGKVKN AYSSSTLFRG 

        70         80         90        100        110        120 
LEIILKGRDP RDAQHFTQRT CGVCTYTHAL ASTRCVDNAV GVHIPKNATY IRNLVLGAQY 

       130        140        150        160        170        180 
LHDHIVHFYH LHALDFVDVT AALKADPAKA AKVASSISPR KTTAADLKAV QDKLKTFVES 

       190        200        210        220        230        240 
GQLGPFTNAY FLGGHPAYYL DPETNLIATA HYLEALRLQV KAARAMAVFG AKNPHTQFTV 

       250        260        270        280        290        300 
VGGVTCYDAL TPQRIAEFEA LWKETKAFVD EVYIPDLLVV AAAYKDWTQY GGTDNFITFG 

       310        320        330        340        350        360 
EFPKDEYDLN SRFFKPGVVF KRDFKNIKPF DKMQIEEHVR HSWYEGAEAR HPWKGQTQPK 

       370        380        390        400        410        420 
YTDLHGDDRY SWMKAPRYMG EPMETGPLAQ VLIAYSQGHP KVKAVTDAVL AKLGVGPEAL 

       430        440        450        460        470        480 
FSTLGRTAAR GIETAVIAEY VGVMLQEYKD NIAKGDNVIC APWEMPKQAE GVGFVNAPRG 

       490        500        510        520        530        540 
GLSHWIRIED GKIGNFQLVV PSTWTLGPRC DKNKLSPVEA SLIGTPVADA KRPVEILRTV 

       550        560 
HSFDPCIACG VHVIDGHTNE VHKFRIL 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F."
Deckers H.M., Wilson F.R., Voordouw G.
J. Gen. Microbiol. 136:2021-2028(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Miyazaki F / DSM 19637.
[3]"Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis."
Higuchi Y., Yagi T., Yasuoka N.
Structure 5:1671-1680(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552.
[4]"Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution."
Higuchi Y., Ogata H., Miki K., Yasuoka N., Yagi T.
Structure 7:549-556(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M58339 Genomic DNA. Translation: AAA23370.1.
CP001197 Genomic DNA. Translation: ACL07227.1.
PIRB45865.
RefSeqYP_002434695.1. NC_011769.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1H2AX-ray1.80L1-567[»]
1H2RX-ray1.40L19-552[»]
1UBHX-ray1.35L19-552[»]
1UBJX-ray1.35L19-552[»]
1UBKX-ray1.18L19-552[»]
1UBLX-ray1.20L19-552[»]
1UBMX-ray1.40L19-552[»]
1UBOX-ray1.35L19-552[»]
1UBRX-ray1.34L19-552[»]
1UBTX-ray1.34L19-552[»]
1UBUX-ray1.35L19-552[»]
1WUHX-ray1.24L19-552[»]
1WUIX-ray1.04L19-552[»]
1WUJX-ray1.40L19-552[»]
1WUKX-ray1.10L19-552[»]
1WULX-ray1.50L19-552[»]
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-247638.
STRING883.DvMF_0270.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACL07227; ACL07227; DvMF_0270.
GeneID7172152.
KEGGdvm:DvMF_0270.
PATRIC21770453. VBIDesVul86729_0281.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0374.
HOGENOMHOG000278799.
KOK00437.
OMAWEMPDEA.
OrthoDBEOG6M9DSB.

Enzyme and pathway databases

BioCycDVUL883:GCJ5-285-MONOMER.

Family and domain databases

Gene3D1.10.645.10. 1 hit.
InterProIPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
IPR029014. NiFe_Hase-like.
[Graphical view]
PfamPF00374. NiFeSe_Hases. 1 hit.
[Graphical view]
SUPFAMSSF56762. SSF56762. 1 hit.
PROSITEPS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP21852.

Entry information

Entry namePHNL_DESVM
AccessionPrimary (citable) accession number: P21852
Secondary accession number(s): B8DPE0
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: April 14, 2009
Last modified: June 11, 2014
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references