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 [NiFeSe] hydrogenase large subunit

Gene
N/A
Organism
Desulfomicrobium baculatum (Desulfovibrio baculatus)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

H2 + A = AH2.

Cofactori

Protein has several cofactor binding sites:
  • Fe cationNote: Binds 2 irons ions. Iron 1 has 3 cyanide and carbon monoxide ligands. Iron 2 has 3 water ligands.
  • Ni2+Note: Binds 1 nickel ion per subunit.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi52Iron 21
Metal bindingi71Nickel1
Metal bindingi74Iron 11
Metal bindingi74Nickel1
Metal bindingi445Iron 2; via carbonyl oxygen1
Metal bindingi493Nickel1
Metal bindingi496Iron 11
Metal bindingi496Nickel1
Metal bindingi499Iron 21

GO - Molecular functioni

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

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001997042 – 514Periplasmic [NiFeSe] hydrogenase large subunitAdd BLAST513

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-6125N.
MINTiMINT-96867.
STRINGi525897.Dbac_1969.

Structurei

Secondary structure

1514
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 19Combined sources6
Beta strandi22 – 25Combined sources4
Beta strandi27 – 34Combined sources8
Beta strandi37 – 45Combined sources9
Helixi51 – 54Combined sources4
Turni55 – 57Combined sources3
Helixi60 – 62Combined sources3
Helixi63 – 66Combined sources4
Helixi67 – 70Combined sources4
Beta strandi72 – 74Combined sources3
Helixi75 – 90Combined sources16
Helixi96 – 120Combined sources25
Helixi123 – 125Combined sources3
Helixi145 – 148Combined sources4
Helixi152 – 184Combined sources33
Beta strandi185 – 189Combined sources5
Beta strandi191 – 194Combined sources4
Beta strandi197 – 200Combined sources4
Helixi204 – 223Combined sources20
Helixi225 – 235Combined sources11
Helixi237 – 240Combined sources4
Beta strandi249 – 251Combined sources3
Beta strandi254 – 258Combined sources5
Beta strandi264 – 266Combined sources3
Beta strandi269 – 272Combined sources4
Beta strandi275 – 277Combined sources3
Helixi281 – 283Combined sources3
Beta strandi284 – 287Combined sources4
Beta strandi296 – 299Combined sources4
Helixi303 – 305Combined sources3
Beta strandi323 – 326Combined sources4
Helixi335 – 342Combined sources8
Helixi348 – 358Combined sources11
Helixi365 – 372Combined sources8
Helixi375 – 399Combined sources25
Beta strandi414 – 424Combined sources11
Beta strandi427 – 436Combined sources10
Beta strandi439 – 447Combined sources9
Helixi449 – 452Combined sources4
Helixi464 – 469Combined sources6
Helixi481 – 489Combined sources9
Helixi494 – 498Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1CC1X-ray2.15L2-499[»]
SMRiP13065.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13065.

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. 2 hits.
[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

        10         20         30         40         50
MSQAATPAAD GKVKISIDPL TRVEGHLKIE VEVKDGKVVD AKCSGGMFRG
60 70 80 90 100
FEQILRGRDP RDSSQIVQRI CGVCPTAHCT ASVMAQDDAF GVKVTTNGRI
110 120 130 140 150
TRNLIFGANY LQSHILHFYH LAALDYVKGP DVSPFVPRYA NADLLTDRIK
160 170 180 190 200
DGAKADATNT YGLNQYLKAL EIRRICHEMV AMFGGRMPHV QGMVVGGATE
210 220 230 240 250
IPTADKVAEY AARFKEVQKF VIEEYLPLIY TLGSVYTDLF ETGIGWKNVI
260 270 280 290 300
AFGVFPEDDD YKTFLLKPGV YIDGKDEEFD SKLVKEYVGH SFFDHSAPGG
310 320 330 340 350
LHYSVGETNP NPDKPGAYSF VKAPRYKDKP CEVGPLARMW VQNPELSPVG
360 370 380 390 400
QKLLKELYGI EAKKFRDLGD KAFSIMGRHV LVAEETWLTA VAVEKWLKQV
410 420 430 440 450
QPGAETYVKS EIPDAAEGTG FTEAPRGALL HYLKIKDKKI ENYQIVSATL
460 470 480 490 500
WNANPRDDMG QRGPIEEALI GVPVPDIKNP VNVGRLVRSY DPULGCAVHV
510
LHAETGEEHV VNID
Length:514
Mass (Da):56,862
Last modified:February 26, 2008 - v3
Checksum:iAC920132081C1ADC
GO

Non-standard residue

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Non-standard residuei493Selenocysteine1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18271 Genomic DNA. Translation: AAA23375.2.
PIRiA33101. HQDVLB.

Keywords - Coding sequence diversityi

Selenocysteine

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18271 Genomic DNA. Translation: AAA23375.2.
PIRiA33101. HQDVLB.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1CC1X-ray2.15L2-499[»]
SMRiP13065.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6125N.
MINTiMINT-96867.
STRINGi525897.Dbac_1969.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105DPX. Bacteria.
COG0374. LUCA.

Miscellaneous databases

EvolutionaryTraceiP13065.

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. 2 hits.
[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 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: November 2, 2016
This is version 98 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

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.