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Entry version 120 (11 Dec 2019)
Sequence version 3 (23 Jan 2007)
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Protein

Biphenyl dioxygenase subunit beta

Gene

bphE

Organism
Paraburkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score:

Annotation score:3 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

The beta subunit may be responsible for the substrate specificity of the enzyme.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: biphenyl degradation

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Biphenyl dioxygenase subunit beta (bphE), Biphenyl dioxygenase subunit alpha (bphA)
  2. Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (bphB)
  3. Biphenyl-2,3-diol 1,2-dioxygenase (bphC)
  4. 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (bphD)
This subpathway is part of the pathway biphenyl degradation, which is itself part of Xenobiotic degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl, the pathway biphenyl degradation and in Xenobiotic degradation.

<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 functionDioxygenase, Oxidoreductase
Biological processAromatic hydrocarbons catabolism
LigandNAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
BXEN266265:BXE_RS42310-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
1.14.12.18 7691

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

More...
UniPathwayi
UPA00155;UER00250

<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_and_taxonomy_section">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:
Biphenyl dioxygenase subunit beta (EC:1.14.12.18)
Alternative name(s):
Biphenyl 2,3-dioxygenase
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:bphE
Ordered Locus Names:Bxeno_C1130
ORF Names:Bxe_C1196
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiParaburkholderia xenovorans (strain LB400)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri266265 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000001817 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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 3

<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 <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000850682 – 188Biphenyl dioxygenase subunit betaAdd BLAST187

<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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterohexamer consisting of three BphA subunits and three BphE subunits. A ferredoxin (BphF) and a ferredoxin reductase (BphG) must be present to obtain activity.

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
266265.Bxe_C1196

<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

1188
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

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SMRi
P37334

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

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PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P37334

<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

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4106DX9 Bacteria
ENOG410YRH3 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000106036

KEGG Orthology (KO)

More...
KOi
K15750

Identification of Orthologs from Complete Genome Data

More...
OMAi
LQAHQFL

Database of Orthologous Groups

More...
OrthoDBi
1736098at2

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00667 ring_hydroxylating_dioxygenases_beta, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR032710 NTF2-like_dom_sf
IPR000391 Rng_hydr_dOase-bsu

The PANTHER Classification System

More...
PANTHERi
PTHR41534 PTHR41534, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00866 Ring_hydroxyl_B, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54427 SSF54427, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P37334-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTNPSPHFFK TFEWPSKAAG LELQNEIEQF YYREAQLLDH RAYEAWFALL
60 70 80 90 100
DKDIHYFMPL RTNRMIREGE LEYSGDQDLA HFDETHETMY GRIRKVTSDV
110 120 130 140 150
GWAENPPSRT RHLVSNVIVK ETATPDTFEV NSAFILYRNR LERQVDIFAG
160 170 180
ERRDVLRRAD NNLGFSIAKR TILLDASTLL SNNLSMFF
Length:188
Mass (Da):22,085
Last modified:January 23, 2007 - v3
<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:i36DBE14E22FEA67B
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 ABE37058 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
M86348 Genomic DNA Translation: AAB63426.1
CP000272 Genomic DNA Translation: ABE37058.1 Different initiation.

NCBI Reference Sequences

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RefSeqi
WP_040123616.1, NZ_CP008761.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABE37058; ABE37058; Bxe_C1196

Database of genes from NCBI RefSeq genomes

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GeneIDi
4010708

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bxb:DR64_8609
bxe:Bxe_C1196

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|266265.5.peg.8946

<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
M86348 Genomic DNA Translation: AAB63426.1
CP000272 Genomic DNA Translation: ABE37058.1 Different initiation.
RefSeqiWP_040123616.1, NZ_CP008761.1

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
2XR8X-ray2.49B/D/F/H/J/L/N/P/R/T/V/X1-188[»]
2XRXX-ray2.42B/D/F/H/J/L/N/P/R/T/V/X1-188[»]
2XSHX-ray2.29B/D/F/H/J/L1-188[»]
2XSOX-ray2.20B/D/F/H/J/L/N/P/R/T/V/X1-188[»]
2YFIX-ray2.15B/D/F/H/J/L1-188[»]
2YFJX-ray2.15B/D/F/H/J/L1-188[»]
2YFLX-ray2.60B/D/F/H/J/L1-188[»]
5AEUX-ray2.49B/D/F/H1-188[»]
5AEWX-ray1.88B/D/F/H/J/L/N/P/R/T/V/X1-188[»]
SMRiP37334
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi266265.Bxe_C1196

Genome annotation databases

EnsemblBacteriaiABE37058; ABE37058; Bxe_C1196
GeneIDi4010708
KEGGibxb:DR64_8609
bxe:Bxe_C1196
PATRICifig|266265.5.peg.8946

Phylogenomic databases

eggNOGiENOG4106DX9 Bacteria
ENOG410YRH3 LUCA
HOGENOMiHOG000106036
KOiK15750
OMAiLQAHQFL
OrthoDBi1736098at2

Enzyme and pathway databases

UniPathwayiUPA00155;UER00250
BioCyciBXEN266265:BXE_RS42310-MONOMER
BRENDAi1.14.12.18 7691

Miscellaneous databases

EvolutionaryTraceiP37334

Family and domain databases

CDDicd00667 ring_hydroxylating_dioxygenases_beta, 1 hit
InterProiView protein in InterPro
IPR032710 NTF2-like_dom_sf
IPR000391 Rng_hydr_dOase-bsu
PANTHERiPTHR41534 PTHR41534, 1 hit
PfamiView protein in Pfam
PF00866 Ring_hydroxyl_B, 1 hit
SUPFAMiSSF54427 SSF54427, 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 nameiBPHE_PARXL
<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: P37334
Secondary accession number(s): Q13FT1
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: January 23, 2007
Last modified: December 11, 2019
This is version 120 of the entry and version 3 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, Direct protein sequencing, 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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