ubiD:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

UbiD

Synonyms

3-octaprenyl-4-hydroxybenzoate decarboxylase[1], YigY[2][1], YigC[2][1], UbiD[2][1], B3843[2][1] , ECK3835, JW3819, yigC, yigY, b3843

Product description

3-octaprenyl-4-hydroxybenzoate decarboxylase[2][3];

Component of 3-octaprenyl-4-hydroxybenzoate decarboxylase[3]

3-octaprenyl-4-hydroxybenzoate carboxylyase; ubiquinone biosynthesis, third step; UbiX isozyme[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0008694

3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity

PMID:4897112[5]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0005886

plasma membrane

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01636

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006744

ubiquinone biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01636

P

Seeded from EcoCyc (v14.0)

complete

GO:0006744

ubiquinone biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0831

P

Seeded from EcoCyc (v14.0)

complete

GO:0008694

3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01636

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of 3-octaprenyl-4-hydroxybenzoate decarboxylase

could be indirect

Protein

yiaG

PMID:16606699[6]

Experiment(s):EBI-1146774

Protein

barA

PMID:16606699[6]

Experiment(s):EBI-1146774
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MDAMKYNDLR DFLTLLEQQG ELKRITLPVD PHLEITEIAD RTLRAGGPAL LFENPKGYSM
PVLCNLFGTP KRVAMGMGQE DVSALREVGK LLAFLKEPEP PKGFRDLFDK LPQFKQVLNM
PTKRLRGAPC QQKIVSGDDV DLNRIPIMTC WPEDAAPLIT WGLTVTRGPH KERQNLGIYR
QQLIGKNKLI MRWLSHRGGA LDYQEWCAAH PGERFPVSVA LGADPATILG AVTPVPDTLS
EYAFAGLLRG TKTEVVKCIS NDLEVPASAE IVLEGYIEQG ETAPEGPYGD HTGYYNEVDS
FPVFTVTHIT QREDAIYHST YTGRPPDEPA VLGVALNEVF VPILQKQFPE IVDFYLPPEG
CSYRLAVVTI KKQYAGHAKR VMMGVWSFLR QFMYTKFVIV CDDDVNARDW NDVIWAITTR
MDPARDTVLV ENTPIDYLDF ASPVSGLGSK MGLDATNKWP GETQREWGRP IKKDPDVVAH
IDAIWDELAI FNNGKSA
Length

497

Mol. Wt

55.604 kDa

pI

5.3 (calculated)

Extinction coefficient

78,840 - 79,715 (calc based on 16 Y, 10 W, and 7 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

13..437

PF01977 3-octaprenyl-4-hydroxybenzoate carboxy-lyase

PMID:19920124[7]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ubiD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131689

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948326

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012557

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AAB4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11396

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11396

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948326

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001363

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1369

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Cox, GB et al. (1969) Biosynthesis of ubiquinone in Escherichia coli K-12: location of genes affecting the metabolism of 3-octaprenyl-4-hydroxybenzoic acid and 2-octaprenylphenol. J. Bacteriol. 99 450-8 PubMed
  6. ↑ 6.0 6.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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