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Protein

Periplasmic [NiFe] hydrogenase large subunit

Gene

hydB

Organism
Desulfovibrio fructosivorans
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 bindingi72NickelSequence analysis1
Metal bindingi75NickelSequence analysis1
Metal bindingi543NickelSequence analysis1
Metal bindingi546NickelSequence analysis1

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 fructosivorans
Taxonomic identifieri878 [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 methionineiRemoved1 Publication
ChainiPRO_00000134012 – 549Periplasmic [NiFe] hydrogenase large subunitAdd BLAST548
PropeptideiPRO_0000013402550 – 564By similarityAdd BLAST15

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6171N.
MINTiMINT-1539432.
STRINGi596151.DesfrDRAFT_3947.

Structurei

Secondary structure

1564
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 18Combined sources5
Beta strandi23 – 26Combined sources4
Beta strandi28 – 35Combined sources8
Beta strandi38 – 46Combined sources9
Helixi52 – 56Combined sources5
Helixi61 – 63Combined sources3
Helixi64 – 68Combined sources5
Helixi69 – 71Combined sources3
Beta strandi73 – 75Combined sources3
Helixi78 – 91Combined sources14
Helixi97 – 121Combined sources25
Helixi124 – 126Combined sources3
Helixi130 – 133Combined sources4
Helixi138 – 148Combined sources11
Helixi153 – 155Combined sources3
Helixi157 – 172Combined sources16
Helixi177 – 179Combined sources3
Turni183 – 186Combined sources4
Helixi195 – 223Combined sources29
Beta strandi224 – 228Combined sources5
Beta strandi236 – 238Combined sources3
Helixi240 – 243Combined sources4
Helixi245 – 264Combined sources20
Helixi266 – 276Combined sources11
Helixi278 – 282Combined sources5
Beta strandi289 – 291Combined sources3
Beta strandi294 – 297Combined sources4
Helixi302 – 308Combined sources7
Beta strandi309 – 311Combined sources3
Beta strandi314 – 316Combined sources3
Helixi329 – 331Combined sources3
Beta strandi332 – 335Combined sources4
Beta strandi339 – 341Combined sources3
Helixi350 – 352Combined sources3
Beta strandi365 – 367Combined sources3
Beta strandi369 – 371Combined sources3
Beta strandi373 – 376Combined sources4
Beta strandi382 – 384Combined sources3
Helixi385 – 394Combined sources10
Helixi398 – 411Combined sources14
Helixi415 – 418Combined sources4
Helixi421 – 452Combined sources32
Beta strandi464 – 474Combined sources11
Beta strandi477 – 486Combined sources10
Beta strandi489 – 496Combined sources8
Helixi498 – 503Combined sources6
Helixi514 – 519Combined sources6
Helixi531 – 539Combined sources9
Helixi544 – 548Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
3H3XX-ray2.70Q/R/S1-549[»]
4UCQX-ray2.60Q/R/S2-549[»]
4UCWX-ray2.30Q/R/S2-549[»]
4UCXX-ray1.95Q/R/S2-549[»]
4UE2X-ray2.02Q/R/S1-549[»]
4UE6X-ray2.30Q/R/S1-549[»]
4UEWX-ray2.08Q/R/S1-549[»]
4UPEX-ray1.80Q/R/S2-549[»]
4UPVX-ray1.52Q/R2-549[»]
4UQLX-ray1.22Q/R2-549[»]
4UQPX-ray1.42Q/R2-549[»]
4URHX-ray1.44Q/R/S2-549[»]
ProteinModelPortaliP18188.
SMRiP18188.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP18188.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105DPX. Bacteria.
COG0374. LUCA.

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.

P18188-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAESKPTPQS TFTGPIVVDP ITRIEGHLRI MVEVENGKVK DAWSSSQLFR
60 70 80 90 100
GLEIILKGRD PRDAQHFTQR ACGVCTYVHA LASSRCVDDA VKVSIPANAR
110 120 130 140 150
MMRNLVMASQ YLHDHLVHFY HLHALDWVDV TAALKADPNK AAKLAASIAP
160 170 180 190 200
ARPGNSAKAL KAVQDKLKAF VESGQLGIFT NAYFLGGHKA YYLPPEVDLI
210 220 230 240 250
ATAHYLEALH MQVKAASAMA ILGGKNPHTQ FTVVGGCSNY QGLTKDPLAN
260 270 280 290 300
YLALSKEVCQ FVNECYIPDL LAVAGFYKDW GGIGGTSNYL AFGEFATDDS
310 320 330 340 350
SPEKHLATSQ FPSGVITGRD LGKVDNVDLG AIYEDVKYSW YAPGGDGKHP
360 370 380 390 400
YDGVTDPKYT KLDDKDHYSW MKAPRYKGKA MEVGPLARTF IAYAKGQPDF
410 420 430 440 450
KKVVDMVLGK LSVPATALHS TLGRTAARGI ETAIVCANME KWIKEMADSG
460 470 480 490 500
AKDNTLCAKW EMPEESKGVG LADAPRGALS HWIRIKGKKI DNFQLVVPST
510 520 530 540 550
WNLGPRGAQG DKSPVEEALI GTPIADPKRP VEILRTVHAF DPCIACGVHV
560
IEPETNEILK FKVC
Length:564
Mass (Da):61,436
Last modified:July 22, 2008 - v4
Checksum:iAB3EBF47F364D849
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35333 Genomic DNA. Translation: AAA23372.2.
PIRiJQ0762. S08199.

Genome annotation databases

PATRICi41172703. VBIDesFru57976_4058.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35333 Genomic DNA. Translation: AAA23372.2.
PIRiJQ0762. S08199.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
3H3XX-ray2.70Q/R/S1-549[»]
4UCQX-ray2.60Q/R/S2-549[»]
4UCWX-ray2.30Q/R/S2-549[»]
4UCXX-ray1.95Q/R/S2-549[»]
4UE2X-ray2.02Q/R/S1-549[»]
4UE6X-ray2.30Q/R/S1-549[»]
4UEWX-ray2.08Q/R/S1-549[»]
4UPEX-ray1.80Q/R/S2-549[»]
4UPVX-ray1.52Q/R2-549[»]
4UQLX-ray1.22Q/R2-549[»]
4UQPX-ray1.42Q/R2-549[»]
4URHX-ray1.44Q/R/S2-549[»]
ProteinModelPortaliP18188.
SMRiP18188.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6171N.
MINTiMINT-1539432.
STRINGi596151.DesfrDRAFT_3947.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

PATRICi41172703. VBIDesFru57976_4058.

Phylogenomic databases

eggNOGiENOG4105DPX. Bacteria.
COG0374. LUCA.

Miscellaneous databases

EvolutionaryTraceiP18188.

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_DESFR
AccessioniPrimary (citable) accession number: P18188
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: July 22, 2008
Last modified: November 2, 2016
This is version 111 of the entry and version 4 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.