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Reviewed, UniProtKB/Swiss-Prot P18188 (PHNL_DESFR)

Last modified June 16, 2009. 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 fructosovorans
Taxonomic identifier878 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

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Protein attributes

Sequence length564 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 H2 + 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-SubCell

   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: UniProtKB-KW

Complete GO annotation...

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 549548Periplasmic [NiFe] hydrogenase large subunit
PRO_0000013401
Propeptide550 – 56415 By similarity
PRO_0000013402

Sites

Metal binding721Nickel Potential
Metal binding751Nickel Potential
Metal binding5431Nickel Potential
Metal binding5461Nickel Potential

Secondary structure

1 .................................................................................... 564
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P18188-1 [UniParc].

Last modified July 22, 2008. Version 4.
Checksum: AB3EBF47F364D849

FASTA56461,436
        10         20         30         40         50         60 
MAESKPTPQS TFTGPIVVDP ITRIEGHLRI MVEVENGKVK DAWSSSQLFR GLEIILKGRD 

        70         80         90        100        110        120 
PRDAQHFTQR ACGVCTYVHA LASSRCVDDA VKVSIPANAR MMRNLVMASQ YLHDHLVHFY 

       130        140        150        160        170        180 
HLHALDWVDV TAALKADPNK AAKLAASIAP ARPGNSAKAL KAVQDKLKAF VESGQLGIFT 

       190        200        210        220        230        240 
NAYFLGGHKA YYLPPEVDLI ATAHYLEALH MQVKAASAMA ILGGKNPHTQ FTVVGGCSNY 

       250        260        270        280        290        300 
QGLTKDPLAN YLALSKEVCQ FVNECYIPDL LAVAGFYKDW GGIGGTSNYL AFGEFATDDS 

       310        320        330        340        350        360 
SPEKHLATSQ FPSGVITGRD LGKVDNVDLG AIYEDVKYSW YAPGGDGKHP YDGVTDPKYT 

       370        380        390        400        410        420 
KLDDKDHYSW MKAPRYKGKA MEVGPLARTF IAYAKGQPDF KKVVDMVLGK LSVPATALHS 

       430        440        450        460        470        480 
TLGRTAARGI ETAIVCANME KWIKEMADSG AKDNTLCAKW EMPEESKGVG LADAPRGALS 

       490        500        510        520        530        540 
HWIRIKGKKI DNFQLVVPST WNLGPRGAQG DKSPVEEALI GTPIADPKRP VEILRTVHAF 

       550        560 
DPCIACGVHV IEPETNEILK FKVC

« Hide

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References

[1]"Cloning and sequencing of the locus encoding the large and small subunit genes of the periplasmic [NiFe]hydrogenase from Desulfovibrio fructosovorans."
Rousset M., Dermoun Z., Matchikian C.E., Belaich J.-P.
Gene 94:95-101(1990) [PubMed: 2227457] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 49200 / DSM 3604 / VKM B-1801 / JJ.
[2]"Characterization of the nickel-iron periplasmic hydrogenase from Desulfovibrio fructosovorans."
Hatchikian C.E., Traore A.S., Fernandez V.M., Cammack R.
Eur. J. Biochem. 187:635-643(1990) [PubMed: 2154378] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-20.
+Additional computationally mapped references.

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Cross-references

Sequence databases

M35333 Genomic DNA. Translation: AAA23372.2.
PIRS08199. JQ0762.

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
1FRFX-ray2.70L1-564[»]
1YQWX-ray1.83Q/R/S1-549[»]
1YRQX-ray2.10H/I/J/K/M/N1-549[»]
3CURX-ray2.40H/I/J1-549[»]
3CUSX-ray2.20Q/R/S1-549[»]
ModBaseSearch...

Protein-protein interaction databases

DIPDIP:6171N.

Enzyme and pathway databases

BRENDA1.12.2.1. 259091.

Family and domain databases

InterProIPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
[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...

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Entry information

Entry namePHNL_DESFR
AccessionPrimary (citable) accession number: P18188
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: July 22, 2008
Last modified: June 16, 2009
This is version 75 of the entry and version 4 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