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Entry version 115 (16 Jan 2019)
Sequence version 1 (01 Mar 2001)
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Protein

Erythronate-4-phosphate dehydrogenase

Gene

pdxB

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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 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 annotation
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. Putative 4-hydroxythreonine-4-phosphate dehydrogenase 2 (PA2212), 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 Publication1
Binding sitei66SubstrateUniRule annotation1 Publication1
Binding sitei146NADUniRule annotation1 Publication1
Binding sitei175NAD; via carbonyl oxygenUniRule annotation1 Publication1
<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 Publication1
Binding sitei232NADUniRule annotation1 Publication1
Active sitei237UniRule annotation1 Publication1
Active sitei254Proton donorUniRule annotation1 Publication1
Binding sitei257NAD; via amide nitrogenUniRule annotation1 Publication1
Binding sitei258SubstrateUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi126 – 127NADUniRule annotation1 Publication2
Nucleotide bindingi206 – 208NADUniRule annotation1 Publication3

<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

  • 4-phosphoerythronate dehydrogenase activity Source: GO_Central
  • NAD binding Source: InterPro
  • protein dimerization activity Source: InterPro

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 functionOxidoreductase
Biological processPyridoxine biosynthesis
LigandNAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
PAER208964:G1FZ6-1401-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
1.1.1.290 5087

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:PA1375
<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>OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
<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 identifieri208964 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
<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
  • UP000002438 <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

Organism-specific databases

Pseudomonas genome database

More...
PseudoCAPi
PA1375

<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

  • cytosol Source: GO_Central

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_00000759821 – 380Erythronate-4-phosphate dehydrogenaseAdd BLAST380

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi65 ↔ 901 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

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

More...
PaxDbi
Q9I3W9

PRoteomics IDEntifications database

More...
PRIDEi
Q9I3W9

<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 annotation2 Publications

GO - Molecular functioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
208964.PA1375

<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

1380
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

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
2O4CX-ray2.30A/B1-380[»]

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
Q9I3W9

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

More...
SMRi
Q9I3W9

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q9I3W9

<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 general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Each subunit can be divided into three discernible structural domains: the lid domain, the nucleotide-binding domain, and the C-terminal dimerization domain. PdxB has a unique dimeric structure among NAD-dependent D-isomer specific 2-hydroxyacid dehydrogenases due to the presence of its dimerization domain at its C-terminus.1 Publication

<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
Q9I3W9

KEGG Orthology (KO)

More...
KOi
K03473

Identification of Orthologs from Complete Genome Data

More...
OMAi
SAPGCNA

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9I3W9

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
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
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.

Q9I3W9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRILADENIP VVDAFFADQG SIRRLPGRAI DRAALAEVDV LLVRSVTEVS
60 70 80 90 100
RAALAGSPVR FVGTCTIGTD HLDLDYFAEA GIAWSSAPGC NARGVVDYVL
110 120 130 140 150
GCLLAMAEVR GADLAERTYG VVGAGQVGGR LVEVLRGLGW KVLVCDPPRQ
160 170 180 190 200
AREPDGEFVS LERLLAEADV ISLHTPLNRD GEHPTRHLLD EPRLAALRPG
210 220 230 240 250
TWLVNASRGA VVDNQALRRL LEGGADLEVA LDVWEGEPQA DPELAARCLI
260 270 280 290 300
ATPHIAGYSL EGKLRGTAQI YQAYCAWRGI AERVSLQDVL PETWLAGLQL
310 320 330 340 350
NPGCDPAWAL ATLCRAVYDP RSDDAAFRRS LTGDSATRRA AFDALRKHYP
360 370 380
PRREITGLRV ATGGQAELQR VVRALGAQLV
Length:380
Mass (Da):41,002
Last modified:March 1, 2001 - 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:i36F6B0F68909D05D
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
AE004091 Genomic DNA Translation: AAG04764.1

Protein sequence database of the Protein Information Resource

More...
PIRi
C83473

NCBI Reference Sequences

More...
RefSeqi
NP_250066.1, NC_002516.2
WP_003112396.1, NC_002516.2

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAG04764; AAG04764; PA1375

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
881132

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
pae:PA1375

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|208964.12.peg.1427

<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
AE004091 Genomic DNA Translation: AAG04764.1
PIRiC83473
RefSeqiNP_250066.1, NC_002516.2
WP_003112396.1, NC_002516.2

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2O4CX-ray2.30A/B1-380[»]
ProteinModelPortaliQ9I3W9
SMRiQ9I3W9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA1375

Proteomic databases

PaxDbiQ9I3W9
PRIDEiQ9I3W9

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG04764; AAG04764; PA1375
GeneIDi881132
KEGGipae:PA1375
PATRICifig|208964.12.peg.1427

Organism-specific databases

PseudoCAPiPA1375

Phylogenomic databases

eggNOGiENOG4105CJ0 Bacteria
COG0111 LUCA
HOGENOMiHOG000234432
InParanoidiQ9I3W9
KOiK03473
OMAiSAPGCNA
PhylomeDBiQ9I3W9

Enzyme and pathway databases

UniPathwayi
UPA00244;UER00310

BioCyciPAER208964:G1FZ6-1401-MONOMER
BRENDAi1.1.1.290 5087

Miscellaneous databases

EvolutionaryTraceiQ9I3W9

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
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
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_PSEAE
<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: Q9I3W9
<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: April 13, 2004
Last sequence update: March 1, 2001
Last modified: January 16, 2019
This is version 115 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, Complete proteome, Reference proteome

Documents

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