Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi72 – 721NickelSequence analysis
Metal bindingi75 – 751NickelSequence analysis
Metal bindingi543 – 5431NickelSequence analysis
Metal bindingi546 – 5461NickelSequence analysis

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)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 549548Periplasmic [NiFe] hydrogenase large subunitPRO_0000013401Add
BLAST
Propeptidei550 – 56415By similarityPRO_0000013402Add
BLAST

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

1
564
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 185Combined sources
Beta strandi23 – 264Combined sources
Beta strandi28 – 358Combined sources
Beta strandi38 – 469Combined sources
Helixi52 – 565Combined sources
Helixi61 – 633Combined sources
Helixi64 – 685Combined sources
Helixi69 – 713Combined sources
Beta strandi73 – 753Combined sources
Helixi78 – 9114Combined sources
Helixi97 – 12125Combined sources
Helixi124 – 1263Combined sources
Helixi130 – 1334Combined sources
Helixi138 – 14811Combined sources
Helixi153 – 1553Combined sources
Helixi157 – 17216Combined sources
Helixi177 – 1793Combined sources
Turni183 – 1864Combined sources
Helixi195 – 22329Combined sources
Beta strandi224 – 2285Combined sources
Beta strandi236 – 2383Combined sources
Helixi240 – 2434Combined sources
Helixi245 – 26420Combined sources
Helixi266 – 27611Combined sources
Helixi278 – 2825Combined sources
Beta strandi289 – 2913Combined sources
Beta strandi294 – 2974Combined sources
Helixi302 – 3087Combined sources
Beta strandi309 – 3113Combined sources
Beta strandi314 – 3163Combined sources
Helixi329 – 3313Combined sources
Beta strandi332 – 3354Combined sources
Beta strandi339 – 3413Combined sources
Helixi350 – 3523Combined sources
Beta strandi365 – 3673Combined sources
Beta strandi369 – 3713Combined sources
Beta strandi373 – 3764Combined sources
Beta strandi382 – 3843Combined sources
Helixi385 – 39410Combined sources
Helixi398 – 41114Combined sources
Helixi415 – 4184Combined sources
Helixi421 – 45232Combined sources
Beta strandi464 – 47411Combined sources
Beta strandi477 – 48610Combined sources
Beta strandi489 – 4968Combined sources
Helixi498 – 5036Combined sources
Helixi514 – 5196Combined sources
Helixi531 – 5399Combined sources
Helixi544 – 5485Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 5-549.
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
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. Positions 5-549.
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: July 6, 2016
This is version 109 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.