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Protein

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

Gene

ubiD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis.UniRule annotation1 Publication

Catalytic activityi

A 4-hydroxy-3-polyprenylbenzoate = a 2-polyprenylphenol + CO2.UniRule annotation1 Publication

Cofactori

Mn2+UniRule annotation1 Publication, prenyl-FMNUniRule annotationNote: Binds 1 prenylated FMN (prenyl-FMN) per subunit.UniRule annotation

Enzyme regulationi

Requires phospholipid, a metal ion, dithiothreitol and at least one other so far unidentified soluble cofactor for maximal activity. Inhibited by EDTA.1 Publication

Pathwayi: ubiquinone biosynthesis

This protein is involved in the pathway ubiquinone biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation1 Publication
View all proteins of this organism that are known to be involved in the pathway ubiquinone biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi175ManganeseUniRule annotation1
Metal bindingi241ManganeseUniRule annotation1
Active sitei290Proton donorUniRule annotation1

GO - Molecular functioni

  • 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity Source: EcoCyc
  • FMN binding Source: InterPro
  • identical protein binding Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • oxidoreductase activity Source: InterPro

GO - Biological processi

  • ubiquinone biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Ubiquinone biosynthesis

Keywords - Ligandi

Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11396-MONOMER.
ECOL316407:JW3819-MONOMER.
MetaCyc:EG11396-MONOMER.
UniPathwayiUPA00232.

Names & Taxonomyi

Protein namesi
Recommended name:
3-octaprenyl-4-hydroxybenzoate carboxy-lyaseUniRule annotation (EC:4.1.1.98UniRule annotation)
Alternative name(s):
Polyprenyl p-hydroxybenzoate decarboxylaseUniRule annotation
Gene namesi
Name:ubiDUniRule annotation
Synonyms:yigC, yigY
Ordered Locus Names:b3843, JW3819
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11396. ubiD.

Subcellular locationi

  • Cell membrane UniRule annotation1 Publication; Peripheral membrane protein UniRule annotation1 Publication

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001573571 – 4973-octaprenyl-4-hydroxybenzoate carboxy-lyaseAdd BLAST497

Proteomic databases

PaxDbiP0AAB4.
PRIDEiP0AAB4.

Interactioni

Subunit structurei

Homohexamer.UniRule annotation2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261466. 301 interactors.
DIPiDIP-48249N.
IntActiP0AAB4. 4 interactors.
STRINGi511145.b3843.

Structurei

Secondary structure

1497
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 18Combined sources10
Beta strandi22 – 25Combined sources4
Helixi34 – 43Combined sources10
Beta strandi49 – 53Combined sources5
Beta strandi62 – 64Combined sources3
Helixi70 – 75Combined sources6
Turni76 – 78Combined sources3
Helixi82 – 84Combined sources3
Helixi85 – 96Combined sources12
Beta strandi123 – 127Combined sources5
Helixi129 – 131Combined sources3
Beta strandi132 – 136Combined sources5
Helixi137 – 139Combined sources3
Helixi142 – 144Combined sources3
Beta strandi163 – 167Combined sources5
Beta strandi174 – 177Combined sources4
Beta strandi181 – 183Combined sources3
Beta strandi185 – 191Combined sources7
Beta strandi195 – 197Combined sources3
Helixi198 – 209Combined sources12
Beta strandi215 – 222Combined sources8
Helixi225 – 232Combined sources8
Helixi241 – 249Combined sources9
Beta strandi254 – 257Combined sources4
Beta strandi259 – 262Combined sources4
Beta strandi264 – 266Combined sources3
Beta strandi270 – 285Combined sources16
Beta strandi293 – 296Combined sources4
Beta strandi299 – 311Combined sources13
Beta strandi324 – 326Combined sources3
Helixi328 – 347Combined sources20
Beta strandi351 – 355Combined sources5
Helixi358 – 360Combined sources3
Turni361 – 363Combined sources3
Beta strandi364 – 370Combined sources7
Helixi377 – 387Combined sources11
Helixi390 – 392Combined sources3
Beta strandi397 – 402Combined sources6
Helixi410 – 419Combined sources10
Helixi423 – 426Combined sources4
Beta strandi427 – 434Combined sources8
Beta strandi442 – 444Combined sources3
Beta strandi447 – 454Combined sources8
Beta strandi463 – 465Combined sources3
Helixi475 – 484Combined sources10
Turni485 – 487Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IDBX-ray2.90A/B/C1-497[»]
ProteinModelPortaliP0AAB4.
SMRiP0AAB4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AAB4.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni175 – 180prenyl-FMN bindingUniRule annotation6
Regioni197 – 198prenyl-FMN bindingUniRule annotation2

Sequence similaritiesi

Belongs to the UbiD family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105D3H. Bacteria.
COG0043. LUCA.
InParanoidiP0AAB4.
KOiK03182.
OMAiDFQEWCQ.
PhylomeDBiP0AAB4.

Family and domain databases

HAMAPiMF_01636. UbiD. 1 hit.
InterProiIPR012349. Split_barrel_FMN-bd.
IPR002830. UbiD.
IPR023677. UbiD_bacteria.
[Graphical view]
PfamiPF01977. UbiD. 1 hit.
[Graphical view]
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00148. TIGR00148. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AAB4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDAMKYNDLR DFLTLLEQQG ELKRITLPVD PHLEITEIAD RTLRAGGPAL
60 70 80 90 100
LFENPKGYSM PVLCNLFGTP KRVAMGMGQE DVSALREVGK LLAFLKEPEP
110 120 130 140 150
PKGFRDLFDK LPQFKQVLNM PTKRLRGAPC QQKIVSGDDV DLNRIPIMTC
160 170 180 190 200
WPEDAAPLIT WGLTVTRGPH KERQNLGIYR QQLIGKNKLI MRWLSHRGGA
210 220 230 240 250
LDYQEWCAAH PGERFPVSVA LGADPATILG AVTPVPDTLS EYAFAGLLRG
260 270 280 290 300
TKTEVVKCIS NDLEVPASAE IVLEGYIEQG ETAPEGPYGD HTGYYNEVDS
310 320 330 340 350
FPVFTVTHIT QREDAIYHST YTGRPPDEPA VLGVALNEVF VPILQKQFPE
360 370 380 390 400
IVDFYLPPEG CSYRLAVVTI KKQYAGHAKR VMMGVWSFLR QFMYTKFVIV
410 420 430 440 450
CDDDVNARDW NDVIWAITTR MDPARDTVLV ENTPIDYLDF ASPVSGLGSK
460 470 480 490
MGLDATNKWP GETQREWGRP IKKDPDVVAH IDAIWDELAI FNNGKSA
Length:497
Mass (Da):55,604
Last modified:September 13, 2005 - v1
Checksum:i5432A3BEBE81ECC5
GO

Sequence cautioni

The sequence AAA67639 differs from that shown. Reason: Frameshift at position 380.Curated
The sequence CAA46146 differs from that shown. Reason: Frameshift at position 376.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti452G → R in AN66; inactive protein. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65013 Genomic DNA. Translation: CAA46146.1. Frameshift.
M87049 Genomic DNA. Translation: AAA67639.1. Frameshift.
M87049 Genomic DNA. Translation: AAA67640.1.
U00096 Genomic DNA. Translation: AAC76846.1.
AP009048 Genomic DNA. Translation: BAE77460.1.
PIRiD65189.
S20905.
S30734.
RefSeqiNP_418285.1. NC_000913.3.
WP_000339804.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76846; AAC76846; b3843.
BAE77460; BAE77460; BAE77460.
GeneIDi948326.
KEGGiecj:JW3819.
eco:b3843.
PATRICi32123183. VBIEscCol129921_3957.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65013 Genomic DNA. Translation: CAA46146.1. Frameshift.
M87049 Genomic DNA. Translation: AAA67639.1. Frameshift.
M87049 Genomic DNA. Translation: AAA67640.1.
U00096 Genomic DNA. Translation: AAC76846.1.
AP009048 Genomic DNA. Translation: BAE77460.1.
PIRiD65189.
S20905.
S30734.
RefSeqiNP_418285.1. NC_000913.3.
WP_000339804.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IDBX-ray2.90A/B/C1-497[»]
ProteinModelPortaliP0AAB4.
SMRiP0AAB4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261466. 301 interactors.
DIPiDIP-48249N.
IntActiP0AAB4. 4 interactors.
STRINGi511145.b3843.

Proteomic databases

PaxDbiP0AAB4.
PRIDEiP0AAB4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76846; AAC76846; b3843.
BAE77460; BAE77460; BAE77460.
GeneIDi948326.
KEGGiecj:JW3819.
eco:b3843.
PATRICi32123183. VBIEscCol129921_3957.

Organism-specific databases

EchoBASEiEB1369.
EcoGeneiEG11396. ubiD.

Phylogenomic databases

eggNOGiENOG4105D3H. Bacteria.
COG0043. LUCA.
InParanoidiP0AAB4.
KOiK03182.
OMAiDFQEWCQ.
PhylomeDBiP0AAB4.

Enzyme and pathway databases

UniPathwayiUPA00232.
BioCyciEcoCyc:EG11396-MONOMER.
ECOL316407:JW3819-MONOMER.
MetaCyc:EG11396-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AAB4.
PROiP0AAB4.

Family and domain databases

HAMAPiMF_01636. UbiD. 1 hit.
InterProiIPR012349. Split_barrel_FMN-bd.
IPR002830. UbiD.
IPR023677. UbiD_bacteria.
[Graphical view]
PfamiPF01977. UbiD. 1 hit.
[Graphical view]
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00148. TIGR00148. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiUBID_ECOLI
AccessioniPrimary (citable) accession number: P0AAB4
Secondary accession number(s): P26615
, P27861, P76767, Q2M8E6, Q47265, Q47714
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 13, 2005
Last sequence update: September 13, 2005
Last modified: November 2, 2016
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.