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P13065 (PHSL_DESBA) Reviewed, UniProtKB/Swiss-Prot

Last modified December 11, 2013. Version 85. 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 [NiFeSe] hydrogenase large subunit

EC=1.12.99.6
Alternative name(s):
NiFeSe hydrogenlyase large chain
OrganismDesulfomicrobium baculatum (Desulfovibrio baculatus)
Taxonomic identifier899 [NCBI]
Taxonomic lineageBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfomicrobiaceaeDesulfomicrobium

Protein attributes

Sequence length514 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

H2 + A = AH2.

Cofactor

Binds 2 irons ions. Iron 1 has 3 cyanide and carbon monoxide ligands. Iron 2 has 3 water ligands.

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.

Ontologies

Keywords
   Cellular componentPeriplasm
   Coding sequence diversitySelenocysteine
   LigandIron
Metal-binding
Nickel
   Molecular functionOxidoreductase
   Technical term3D-structure
Gene Ontology (GO)
   Cellular_componentperiplasmic space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionferredoxin hydrogenase activity

Inferred from electronic annotation. Source: InterPro

hydrogenase (acceptor) activity

Inferred from electronic annotation. Source: UniProtKB-EC

nickel cation binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 514513Periplasmic [NiFeSe] hydrogenase large subunit
PRO_0000199704

Sites

Metal binding521Iron 2
Metal binding711Nickel
Metal binding741Iron 1
Metal binding741Nickel
Metal binding4451Iron 2; via carbonyl oxygen
Metal binding4931Nickel
Metal binding4961Iron 1
Metal binding4961Nickel
Metal binding4991Iron 2

Amino acid modifications

Non-standard residue4931Selenocysteine

Secondary structure

............................................................................... 514
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P13065 [UniParc].

Last modified February 26, 2008. Version 3.
Checksum: AC920132081C1ADC

FASTA51456,862
        10         20         30         40         50         60 
MSQAATPAAD GKVKISIDPL TRVEGHLKIE VEVKDGKVVD AKCSGGMFRG FEQILRGRDP 

        70         80         90        100        110        120 
RDSSQIVQRI CGVCPTAHCT ASVMAQDDAF GVKVTTNGRI TRNLIFGANY LQSHILHFYH 

       130        140        150        160        170        180 
LAALDYVKGP DVSPFVPRYA NADLLTDRIK DGAKADATNT YGLNQYLKAL EIRRICHEMV 

       190        200        210        220        230        240 
AMFGGRMPHV QGMVVGGATE IPTADKVAEY AARFKEVQKF VIEEYLPLIY TLGSVYTDLF 

       250        260        270        280        290        300 
ETGIGWKNVI AFGVFPEDDD YKTFLLKPGV YIDGKDEEFD SKLVKEYVGH SFFDHSAPGG 

       310        320        330        340        350        360 
LHYSVGETNP NPDKPGAYSF VKAPRYKDKP CEVGPLARMW VQNPELSPVG QKLLKELYGI 

       370        380        390        400        410        420 
EAKKFRDLGD KAFSIMGRHV LVAEETWLTA VAVEKWLKQV QPGAETYVKS EIPDAAEGTG 

       430        440        450        460        470        480 
FTEAPRGALL HYLKIKDKKI ENYQIVSATL WNANPRDDMG QRGPIEEALI GVPVPDIKNP 

       490        500        510 
VNVGRLVRSY DPULGCAVHV LHAETGEEHV VNID 

« Hide

References

[1]"Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus."
Menon N.K., Peck H.D. Jr., le Gall J., Przybyla A.E.
J. Bacteriol. 169:5401-5407(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]Erratum
Menon N.K., Pect H.D. Jr., le Gall J., Przybyla A.E.
J. Bacteriol. 170:4429-4429(1988)
Cited for: SEQUENCE REVISION.
[3]"The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center."
Garcin E., Vernede X., Hatchikian E.C., Volbeda A., Frey M., Fontecilla-Camps J.-C.
Structure 7:557-566(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS), SELENOCYSTEINE AT SEC-493.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M18271 Genomic DNA. Translation: AAA23375.2.
PIRHQDVLB. A33101.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CC1X-ray2.15L2-499[»]
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-6125N.
MINTMINT-96867.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

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...

Other

EvolutionaryTraceP13065.

Entry information

Entry namePHSL_DESBA
AccessionPrimary (citable) accession number: P13065
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: February 26, 2008
Last modified: December 11, 2013
This is version 85 of the entry and version 3 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