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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)DescriptionActionsGraphical viewLength
Metal bindingi65Nickel1 Publication1
Metal bindingi68Nickel1
Metal bindingi530Nickel1 Publication1
Metal bindingi533Nickel1

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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00000134032 – 536Periplasmic [NiFe] hydrogenase large subunitAdd BLAST535
PropeptideiPRO_0000013404537 – 551Add BLAST15

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Structurei

Secondary structure

1551
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 11Combined sources4
Beta strandi16 – 19Combined sources4
Beta strandi21 – 28Combined sources8
Beta strandi31 – 39Combined sources9
Helixi45 – 49Combined sources5
Helixi54 – 56Combined sources3
Helixi57 – 62Combined sources6
Beta strandi66 – 68Combined sources3
Helixi71 – 84Combined sources14
Helixi90 – 114Combined sources25
Helixi117 – 119Combined sources3
Helixi124 – 128Combined sources5
Helixi131 – 141Combined sources11
Helixi148 – 163Combined sources16
Helixi168 – 170Combined sources3
Turni174 – 177Combined sources4
Helixi186 – 214Combined sources29
Beta strandi215 – 219Combined sources5
Helixi231 – 234Combined sources4
Helixi236 – 255Combined sources20
Helixi257 – 267Combined sources11
Helixi268 – 273Combined sources6
Beta strandi280 – 282Combined sources3
Helixi293 – 295Combined sources3
Beta strandi296 – 298Combined sources3
Beta strandi301 – 303Combined sources3
Beta strandi307 – 312Combined sources6
Helixi316 – 318Combined sources3
Beta strandi319 – 322Combined sources4
Turni324 – 327Combined sources4
Beta strandi328 – 331Combined sources4
Helixi336 – 338Combined sources3
Helixi350 – 352Combined sources3
Beta strandi355 – 357Combined sources3
Beta strandi359 – 362Combined sources4
Helixi371 – 380Combined sources10
Helixi384 – 397Combined sources14
Helixi401 – 404Combined sources4
Helixi407 – 437Combined sources31
Beta strandi451 – 461Combined sources11
Beta strandi464 – 473Combined sources10
Beta strandi476 – 483Combined sources8
Helixi485 – 490Combined sources6
Helixi501 – 506Combined sources6
Helixi518 – 526Combined sources9
Helixi531 – 535Combined sources5

3D structure databases

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

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: November 2, 2016
This is version 104 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.