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P13065

- PHSL_DESBA

UniProt

P13065 - PHSL_DESBA

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Protein
Periplasmic [NiFeSe] hydrogenase large subunit
Gene
N/A
Organism
Desulfomicrobium baculatum (Desulfovibrio baculatus)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

H2 + A = AH2.

Cofactori

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi52 – 521Iron 2
Metal bindingi71 – 711Nickel
Metal bindingi74 – 741Iron 1
Metal bindingi74 – 741Nickel
Metal bindingi445 – 4451Iron 2; via carbonyl oxygen
Metal bindingi493 – 4931Nickel
Metal bindingi496 – 4961Iron 1
Metal bindingi496 – 4961Nickel
Metal bindingi499 – 4991Iron 2

GO - Molecular functioni

  1. ferredoxin hydrogenase activity Source: InterPro
  2. hydrogenase (acceptor) activity Source: UniProtKB-EC
  3. nickel cation binding Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Nickel

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [NiFeSe] hydrogenase large subunit (EC:1.12.99.6)
Alternative name(s):
NiFeSe hydrogenlyase large chain
OrganismiDesulfomicrobium baculatum (Desulfovibrio baculatus)
Taxonomic identifieri899 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfomicrobiaceaeDesulfomicrobium

Subcellular locationi

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 514513Periplasmic [NiFeSe] hydrogenase large subunit
PRO_0000199704Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6125N.
MINTiMINT-96867.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 196
Beta strandi22 – 254
Beta strandi27 – 348
Beta strandi37 – 459
Helixi51 – 544
Turni55 – 573
Helixi60 – 623
Helixi63 – 664
Helixi67 – 704
Beta strandi72 – 743
Helixi75 – 9016
Helixi96 – 12025
Helixi123 – 1253
Helixi145 – 1484
Helixi152 – 18433
Beta strandi185 – 1895
Beta strandi191 – 1944
Beta strandi197 – 2004
Helixi204 – 22320
Helixi225 – 23511
Helixi237 – 2404
Beta strandi249 – 2513
Beta strandi254 – 2585
Beta strandi264 – 2663
Beta strandi269 – 2724
Beta strandi275 – 2773
Helixi281 – 2833
Beta strandi284 – 2874
Beta strandi296 – 2994
Helixi303 – 3053
Beta strandi323 – 3264
Helixi335 – 3428
Helixi348 – 35811
Helixi365 – 3728
Helixi375 – 39925
Beta strandi414 – 42411
Beta strandi427 – 43610
Beta strandi439 – 4479
Helixi449 – 4524
Helixi464 – 4696
Helixi481 – 4899
Helixi494 – 4985

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CC1X-ray2.15L2-499[»]

Miscellaneous databases

EvolutionaryTraceiP13065.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di1.10.645.10. 1 hit.
InterProiIPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
IPR029014. NiFe_Hase-like.
[Graphical view]
PfamiPF00374. NiFeSe_Hases. 1 hit.
[Graphical view]
SUPFAMiSSF56762. SSF56762. 1 hit.
PROSITEiPS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P13065-1 [UniParc]FASTAAdd to Basket

« Hide

MSQAATPAAD GKVKISIDPL TRVEGHLKIE VEVKDGKVVD AKCSGGMFRG    50
FEQILRGRDP RDSSQIVQRI CGVCPTAHCT ASVMAQDDAF GVKVTTNGRI 100
TRNLIFGANY LQSHILHFYH LAALDYVKGP DVSPFVPRYA NADLLTDRIK 150
DGAKADATNT YGLNQYLKAL EIRRICHEMV AMFGGRMPHV QGMVVGGATE 200
IPTADKVAEY AARFKEVQKF VIEEYLPLIY TLGSVYTDLF ETGIGWKNVI 250
AFGVFPEDDD YKTFLLKPGV YIDGKDEEFD SKLVKEYVGH SFFDHSAPGG 300
LHYSVGETNP NPDKPGAYSF VKAPRYKDKP CEVGPLARMW VQNPELSPVG 350
QKLLKELYGI EAKKFRDLGD KAFSIMGRHV LVAEETWLTA VAVEKWLKQV 400
QPGAETYVKS EIPDAAEGTG FTEAPRGALL HYLKIKDKKI ENYQIVSATL 450
WNANPRDDMG QRGPIEEALI GVPVPDIKNP VNVGRLVRSY DPULGCAVHV 500
LHAETGEEHV VNID 514
Length:514
Mass (Da):56,862
Last modified:February 26, 2008 - v3
Checksum:iAC920132081C1ADC
GO

Non-standard residue

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Non-standard residuei493 – 4931Selenocysteine

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M18271 Genomic DNA. Translation: AAA23375.2.
PIRiA33101. HQDVLB.

Keywords - Coding sequence diversityi

Selenocysteine

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M18271 Genomic DNA. Translation: AAA23375.2 .
PIRi A33101. HQDVLB.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1CC1 X-ray 2.15 L 2-499 [» ]
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6125N.
MINTi MINT-96867.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P13065.

Family and domain databases

Gene3Di 1.10.645.10. 1 hit.
InterProi IPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
IPR029014. NiFe_Hase-like.
[Graphical view ]
Pfami PF00374. NiFeSe_Hases. 1 hit.
[Graphical view ]
SUPFAMi SSF56762. SSF56762. 1 hit.
PROSITEi PS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiPHSL_DESBA
AccessioniPrimary (citable) accession number: P13065
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: February 26, 2008
Last modified: June 11, 2014
This is version 86 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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