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Protein

Periplasmic [NiFe] hydrogenase large subunit

Gene

hydB

Organism
Desulfovibrio gigas
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Ni2+Note: Binds 1 nickel ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi65 – 651Nickel1 Publication
Metal bindingi68 – 681Nickel
Metal bindingi530 – 5301Nickel1 Publication
Metal bindingi533 – 5331Nickel

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Metal-binding, Nickel

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [NiFe] hydrogenase large subunit (EC:1.12.2.1)
Alternative name(s):
NiFe hydrogenlyase large chain
Gene namesi
Name:hydB
OrganismiDesulfovibrio gigas
Taxonomic identifieri879 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 536535Periplasmic [NiFe] hydrogenase large subunitPRO_0000013403Add
BLAST
Propeptidei537 – 55115PRO_0000013404Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Structurei

Secondary structure

1
551
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 114Combined sources
Beta strandi16 – 194Combined sources
Beta strandi21 – 288Combined sources
Beta strandi31 – 399Combined sources
Helixi45 – 495Combined sources
Helixi54 – 563Combined sources
Helixi57 – 626Combined sources
Beta strandi66 – 683Combined sources
Helixi71 – 8414Combined sources
Helixi90 – 11425Combined sources
Helixi117 – 1193Combined sources
Helixi124 – 1285Combined sources
Helixi131 – 14111Combined sources
Helixi148 – 16316Combined sources
Helixi168 – 1703Combined sources
Turni174 – 1774Combined sources
Helixi186 – 21429Combined sources
Beta strandi215 – 2195Combined sources
Helixi231 – 2344Combined sources
Helixi236 – 25520Combined sources
Helixi257 – 26711Combined sources
Helixi268 – 2736Combined sources
Beta strandi280 – 2823Combined sources
Helixi293 – 2953Combined sources
Beta strandi296 – 2983Combined sources
Beta strandi301 – 3033Combined sources
Beta strandi307 – 3126Combined sources
Helixi316 – 3183Combined sources
Beta strandi319 – 3224Combined sources
Turni324 – 3274Combined sources
Beta strandi328 – 3314Combined sources
Helixi336 – 3383Combined sources
Helixi350 – 3523Combined sources
Beta strandi355 – 3573Combined sources
Beta strandi359 – 3624Combined sources
Helixi371 – 38010Combined sources
Helixi384 – 39714Combined sources
Helixi401 – 4044Combined sources
Helixi407 – 43731Combined sources
Beta strandi451 – 46111Combined sources
Beta strandi464 – 47310Combined sources
Beta strandi476 – 4838Combined sources
Helixi485 – 4906Combined sources
Helixi501 – 5066Combined sources
Helixi518 – 5269Combined sources
Helixi531 – 5355Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85B/D1-536[»]
1YQ9X-ray2.35H/I1-536[»]
2FRVX-ray2.54B/D/F/H/J/L1-536[»]
ProteinModelPortaliP12944.
SMRiP12944. Positions 7-536.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12944.

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.

P12944-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEMQGNKIV VDPITRIEGH LRIEVEVEGG KIKNAWSMST LFRGLEMILK
60 70 80 90 100
GRDPRDAQHF TQRACGVCTY VHALASVRAV DNCVGVKIPE NATLMRNLTM
110 120 130 140 150
GAQYMHDHLV HFYHLHALDW VNVANALNAD PAKAARLAND LSPRKTTTES
160 170 180 190 200
LKAVQAKVKA LVESGQLGIF TNAYFLGGHP AYVLPAEVDL IATAHYLEAL
210 220 230 240 250
RVQVKAARAM AIFGAKNPHT QFTVVGGCTN YDSLRPERIA EFRKLYKEVR
260 270 280 290 300
EFIEQVYITD LLAVAGFYKN WAGIGKTSNF LTCGEFPTDE YDLNSRYTPQ
310 320 330 340 350
GVIWGNDLSK VDDFNPDLIE EHVKYSWYEG ADAHHPYKGV TKPKWTEFHG
360 370 380 390 400
EDRYSWMKAP RYKGEAFEVG PLASVLVAYA KKHEPTVKAV DLVLKTLGVG
410 420 430 440 450
PEALFSTLGR TAARGIQCLT AAQEVEVWLD KLEANVKAGK DDLYTDWQYP
460 470 480 490 500
TESQGVGFVN APRGMLSHWI VQRGGKIENF QHVVPSTWNL GPRCAERKLS
510 520 530 540 550
AVEQALIGTP IADPKRPVEI LRTVHSYDPC IACGVHVIDP ESNQVHKFRI

L
Length:551
Mass (Da):61,480
Last modified:January 23, 2007 - v3
Checksum:i4CF99AD3F75189B0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18083 Genomic DNA. Translation: AAA23378.1. Sequence problems.
PIRiB32315. HQDVLG.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18083 Genomic DNA. Translation: AAA23378.1. Sequence problems.
PIRiB32315. HQDVLG.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85B/D1-536[»]
1YQ9X-ray2.35H/I1-536[»]
2FRVX-ray2.54B/D/F/H/J/L1-536[»]
ProteinModelPortaliP12944.
SMRiP12944. Positions 7-536.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP12944.

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]
ProtoNetiSearch...

Publicationsi

  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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
  3. 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] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).

Entry informationi

Entry nameiPHNL_DESGI
AccessioniPrimary (citable) accession number: P12944
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 102 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, Direct protein sequencing

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.