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UniProtKB - P05459 (PDXB_ECOLI)

Entry version 162 (13 Feb 2019)
Sequence version 2 (01 Apr 1990)
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Protein

Erythronate-4-phosphate dehydrogenase

Gene

pdxB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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 transcript 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 oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate.UniRule annotation

<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: pyridoxine 5'-phosphate biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.UniRule annotation1 Publication
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. D-erythrose-4-phosphate dehydrogenase (epd)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ)
This subpathway is part of the pathway pyridoxine 5'-phosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate, the pathway pyridoxine 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei45SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Binding sitei146NADUniRule annotation1
Binding sitei175NAD; via carbonyl oxygenUniRule annotation1
<p>This subsection of the ‘Function’ 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 sitei208UniRule annotation1
Binding sitei232NADUniRule annotation1
Active sitei237UniRule annotation1
Active sitei254Proton donorUniRule annotation1
Binding sitei257NAD; via amide nitrogenUniRule annotation1
Binding sitei258SubstrateUniRule annotation1

<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

View the complete GO annotation on QuickGO ...

GO - Biological processi

  • 'de novo' pyridoxal 5'-phosphate biosynthetic process Source: EcoCyc
  • pyridoxine biosynthetic process Source: EcoCyc
View the complete GO annotation on QuickGO ...

<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 functionOxidoreductase
Biological processPyridoxine biosynthesis
LigandNAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:ERYTHRON4PDEHYDROG-MONOMER
ECOL316407:JW2317-MONOMER
MetaCyc:ERYTHRON4PDEHYDROG-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		1.1.1.290 2026

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

More...UniPathwayi
UPA00244;UER00310

<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:
Erythronate-4-phosphate dehydrogenaseUniRule annotation (EC:1.1.1.290UniRule annotation)
<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:pdxBUniRule annotation
Ordered Locus Names:b2320, JW2317
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...EcoGenei		EG10692 pdxB

<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

View the complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cytoplasm

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000759751 – 378Erythronate-4-phosphate dehydrogenaseAdd BLAST378

Proteomic databases

Encyclopedia of Proteome Dynamics

More...EPDi		P05459

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P05459

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

More...PaxDbi		P05459

PRoteomics IDEntifications database

More...PRIDEi		P05459

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

During growth rate.1 Publication

<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

Homodimer.UniRule annotation

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4259616, 24 interactors

Database of interacting proteins

More...DIPi		DIP-10449N

Protein interaction database and analysis system

More...IntActi		P05459, 9 interactors

STRING: functional protein association networks

More...STRINGi		316385.ECDH10B_2482

<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

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...ProteinModelPortali		P05459

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

More...SMRi		P05459

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<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

Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105CJ0 Bacteria
COG0111 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000234432

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P05459

KEGG Orthology (KO)

More...KOi		K03473

Database for complete collections of gene phylogenies

More...PhylomeDBi		P05459

Family and domain databases

Conserved Domains Database

More...CDDi		cd12158 ErythrP_dh, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.1370.170, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01825 PdxB, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR006139 D-isomer_2_OHA_DH_cat_dom
IPR029753 D-isomer_DH_CS
IPR029752 D-isomer_DH_CS1
IPR006140 D-isomer_DH_NAD-bd
IPR020921 Erythronate-4-P_DHase
IPR024531 Erythronate-4-P_DHase_dimer
IPR036291 NAD(P)-bd_dom_sf
IPR038251 PdxB_dimer_sf

The PANTHER Classification System

More...PANTHERi		PTHR42938:SF3 PTHR42938:SF3, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00389 2-Hacid_dh, 1 hit
PF02826 2-Hacid_dh_C, 1 hit
PF11890 DUF3410, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF51735 SSF51735, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00065 D_2_HYDROXYACID_DH_1, 1 hit
PS00671 D_2_HYDROXYACID_DH_3, 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>.<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.

P05459-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKILVDENMP YARDLFSRLG EVTAVPGRPI PVAQLADADA LMVRSVTKVN 
        60         70         80         90        100
ESLLAGKPIK FVGTATAGTD HVDEAWLKQA GIGFSAAPGC NAIAVVEYVF 
       110        120        130        140        150
SSLLMLAERD GFSLYDRTVG IVGVGNVGRR LQARLEALGI KTLLCDPPRA 
       160        170        180        190        200
DRGDEGDFRS LDELVQRADI LTFHTPLFKD GPYKTLHLAD EKLIRSLKPG 
       210        220        230        240        250
AILINACRGA VVDNTALLTC LNEGQKLSVV LDVWEGEPEL NVELLKKVDI 
       260        270        280        290        300
GTSHIAGYTL EGKARGTTQV FEAYSKFIGH EQHVALDTLL PAPEFGRITL 
       310        320        330        340        350
HGPLDQPTLK RLVHLVYDVR RDDAPLRKVA GIPGEFDKLR KNYLERREWS 
       360        370 
SLYVICDDAS AASLLCKLGF NAVHHPAR
Length:378
Mass (Da):41,368
Last modified:April 1, 1990 - v2
<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:i6CEF17691CF2C14A
GO

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
M29962 Genomic DNA Translation: AAA24308.1
U76961 Genomic DNA Translation: AAB36530.1
U00096 Genomic DNA Translation: AAC75380.1
AP009048 Genomic DNA Translation: BAA16177.1
X02743 Genomic DNA Translation: CAA26520.1
M15541 Genomic DNA Translation: AAA24310.1

Protein sequence database of the Protein Information Resource

More...PIRi		JV0051 DEECPP

NCBI Reference Sequences

More...RefSeqi		NP_416823.1, NC_000913.3
WP_000699148.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75380; AAC75380; b2320
BAA16177; BAA16177; BAA16177

Database of genes from NCBI RefSeq genomes

More...GeneIDi		946785

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW2317
eco:b2320

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.4413

<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
M29962 Genomic DNA Translation: AAA24308.1
U76961 Genomic DNA Translation: AAB36530.1
U00096 Genomic DNA Translation: AAC75380.1
AP009048 Genomic DNA Translation: BAA16177.1
X02743 Genomic DNA Translation: CAA26520.1
M15541 Genomic DNA Translation: AAA24310.1
PIRiJV0051 DEECPP
RefSeqiNP_416823.1, NC_000913.3
WP_000699148.1, NZ_LN832404.1

3D structure databases

ProteinModelPortaliP05459
SMRiP05459
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259616, 24 interactors
DIPiDIP-10449N
IntActiP05459, 9 interactors
STRINGi316385.ECDH10B_2482

Proteomic databases

EPDiP05459
jPOSTiP05459
PaxDbiP05459
PRIDEiP05459

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75380; AAC75380; b2320
BAA16177; BAA16177; BAA16177
GeneIDi946785
KEGGiecj:JW2317
eco:b2320
PATRICifig|1411691.4.peg.4413

Organism-specific databases

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

More...EchoBASEi		EB0686
EcoGeneiEG10692 pdxB

Phylogenomic databases

eggNOGiENOG4105CJ0 Bacteria
COG0111 LUCA
HOGENOMiHOG000234432
InParanoidiP05459
KOiK03473
PhylomeDBiP05459

Enzyme and pathway databases

UniPathwayi
UPA00244;UER00310

BioCyciEcoCyc:ERYTHRON4PDEHYDROG-MONOMER
ECOL316407:JW2317-MONOMER
MetaCyc:ERYTHRON4PDEHYDROG-MONOMER
BRENDAi1.1.1.290 2026

Miscellaneous databases

Protein Ontology

More...PROi		PR:P05459

Family and domain databases

CDDicd12158 ErythrP_dh, 1 hit
Gene3Di3.30.1370.170, 1 hit
HAMAPiMF_01825 PdxB, 1 hit
InterProiView protein in InterPro
IPR006139 D-isomer_2_OHA_DH_cat_dom
IPR029753 D-isomer_DH_CS
IPR029752 D-isomer_DH_CS1
IPR006140 D-isomer_DH_NAD-bd
IPR020921 Erythronate-4-P_DHase
IPR024531 Erythronate-4-P_DHase_dimer
IPR036291 NAD(P)-bd_dom_sf
IPR038251 PdxB_dimer_sf
PANTHERiPTHR42938:SF3 PTHR42938:SF3, 1 hit
PfamiView protein in Pfam
PF00389 2-Hacid_dh, 1 hit
PF02826 2-Hacid_dh_C, 1 hit
PF11890 DUF3410, 1 hit
SUPFAMiSSF51735 SSF51735, 1 hit
PROSITEiView protein in PROSITE
PS00065 D_2_HYDROXYACID_DH_1, 1 hit
PS00671 D_2_HYDROXYACID_DH_3, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		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 nameiPDXB_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: P05459
<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: November 1, 1988
Last sequence update: April 1, 1990
Last modified: February 13, 2019
This is version 162 of the entry and version 2 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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