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Entry version 124 (02 Dec 2020)
Sequence version 1 (13 Sep 2005)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity 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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi175ManganeseUniRule annotationCombined sources1 Publication1
Metal bindingi241ManganeseUniRule annotationCombined sources1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei290Proton acceptorUniRule annotation1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDecarboxylase, Lyase
Biological processUbiquinone biosynthesis
LigandFlavoprotein, FMN, Manganese, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11396-MONOMER
MetaCyc:EG11396-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00232

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
3-octaprenyl-4-hydroxybenzoate carboxy-lyase1 PublicationUniRule annotation (EC:4.1.1.98UniRule annotation1 Publication)
Alternative name(s):
Polyprenyl p-hydroxybenzoate decarboxylaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ubiDUniRule annotation
Synonyms:yigC, yigY
Ordered Locus Names:b3843, JW3819
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cell membrane, Membrane

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001573571 – 4973-octaprenyl-4-hydroxybenzoate carboxy-lyaseAdd BLAST497

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P0AAB4

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P0AAB4

PRoteomics IDEntifications database

More...
PRIDEi
P0AAB4

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homohexamer.

UniRule annotation2 Publications1 Publication

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261466, 338 interactors
852623, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-48249N

Protein interaction database and analysis system

More...
IntActi
P0AAB4, 4 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3843

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1497
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P0AAB4

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P0AAB4

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni178 – 180Prenyl-FMN bindingUniRule annotationCombined sources1 Publication3
Regioni192 – 194Prenyl-FMN bindingUniRule annotationCombined sources1 Publication3
Regioni197 – 198Prenyl-FMN bindingUniRule annotationCombined sources1 Publication2

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the UbiD family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0043, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_023348_4_1_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0AAB4

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0AAB4

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01636, UbiD, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002830, UbiD
IPR023677, UbiD_bacteria

The PANTHER Classification System

More...
PANTHERi
PTHR30108, PTHR30108, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01977, UbiD, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00148, TIGR00148, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i5432A3BEBE81ECC5
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA67639 differs from that shown. Reason: Frameshift.Curated
The sequence CAA46146 differs from that shown. Reason: Frameshift.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural varianti452G → R in AN66; inactive protein. 1 Publication1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
D65189
S20905
S30734

NCBI Reference Sequences

More...
RefSeqi
NP_418285.1, NC_000913.3
WP_000339804.1, NZ_STEB01000021.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76846; AAC76846; b3843
BAE77460; BAE77460; BAE77460

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
49586873
948326

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3819
eco:b3843

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.2867

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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_STEB01000021.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2IDBX-ray2.90A/B/C1-497[»]
5M1BX-ray3.15A/B/C1-497[»]
5M1CX-ray2.75A/B/C1-497[»]
5M1DX-ray2.70A/B/C1-497[»]
5M1EX-ray2.62A/B/C1-497[»]
SMRiP0AAB4
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4261466, 338 interactors
852623, 1 interactor
DIPiDIP-48249N
IntActiP0AAB4, 4 interactors
STRINGi511145.b3843

Proteomic databases

jPOSTiP0AAB4
PaxDbiP0AAB4
PRIDEiP0AAB4

Genome annotation databases

EnsemblBacteriaiAAC76846; AAC76846; b3843
BAE77460; BAE77460; BAE77460
GeneIDi49586873
948326
KEGGiecj:JW3819
eco:b3843
PATRICifig|1411691.4.peg.2867

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB1369

Phylogenomic databases

eggNOGiCOG0043, Bacteria
HOGENOMiCLU_023348_4_1_6
InParanoidiP0AAB4
PhylomeDBiP0AAB4

Enzyme and pathway databases

UniPathwayiUPA00232
BioCyciEcoCyc:EG11396-MONOMER
MetaCyc:EG11396-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0AAB4

Protein Ontology

More...
PROi
PR:P0AAB4

Family and domain databases

HAMAPiMF_01636, UbiD, 1 hit
InterProiView protein in InterPro
IPR002830, UbiD
IPR023677, UbiD_bacteria
PANTHERiPTHR30108, PTHR30108, 1 hit
PfamiView protein in Pfam
PF01977, UbiD, 1 hit
TIGRFAMsiTIGR00148, TIGR00148, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiUBID_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0AAB4
Secondary accession number(s): P26615
, P27861, P76767, Q2M8E6, Q47265, Q47714
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 13, 2005
Last sequence update: September 13, 2005
Last modified: December 2, 2020
This is version 124 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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