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UniProtKB - P25906 (PDXI_ECOLI)

Entry version 146 (25 May 2022)
Sequence version 1 (01 May 1992)
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Protein

Pyridoxine 4-dehydrogenase

Gene

pdxI

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 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 NAD(P)H-dependent reduction of pyridoxal to pyridoxine in vitro. Is not able to reduce 4-pyridoxate, and to oxidize pyridoxine or pyridoxamine (PubMed:27941785).

Has Kemp eliminase activity towards the non-physiological substrate 5-nitrobenzisoxazole, producing 4-nitro-2-cyanophenol; this activity is not considered to be physiologically relevant (PubMed:21332126).

2 Publications

<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 describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 0.11 sec(-1) for the Kemp eliminase activity towards 5-nitrobenzisoxazole.1 Publication
  1. KM=270 µM for 5-nitrobenzisoxazole1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<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 sitei59Proton donorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 bindingi210 – 218NADPBy similarity9

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

  • pyridoxal 5'-phosphate salvage Source: EcoCyc
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
LigandNAD, NADP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11309-MONOMER

<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:
Pyridoxine 4-dehydrogenase1 Publication (EC:1.1.1.651 Publication)
<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:pdxI1 Publication
Synonyms:ydbCImported
Ordered Locus Names:b1406, JW1403
<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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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

<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_00000703931 – 286Pyridoxine 4-dehydrogenaseAdd BLAST286

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P25906

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

More...PaxDbi		P25906

PRoteomics IDEntifications database

More...PRIDEi		P25906

2D gel databases

Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

More...SWISS-2DPAGEi		P25906

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4263019, 15 interactors

Database of interacting proteins

More...DIPi		DIP-11632N

Protein interaction database and analysis system

More...IntActi		P25906, 4 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1406

<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

AlphaFold Protein Structure Database

More...AlphaFoldDBi		P25906

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

More...SMRi		P25906

Database of comparative protein structure models

More...ModBasei		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 aldo/keto reductase family. Aldo/keto reductase 2 subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0667, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_023205_2_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P25906

Identification of Orthologs from Complete Genome Data

More...OMAi		GYGTMQL

Database for complete collections of gene phylogenies

More...PhylomeDBi		P25906

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.20.20.100, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR023210, NADP_OxRdtase_dom
IPR036812, NADP_OxRdtase_dom_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00248, Aldo_ket_red, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF51430, SSF51430, 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.

P25906-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSNTFTLGT KSVNRLGYGA MQLAGPGVFG PPRDRHVAIT VLREALALGV 
        60         70         80         90        100
NHIDTSDFYG PHVTNQIIRE ALYPYSDDLT IVTKIGARRG EDASWLPAFS 
       110        120        130        140        150
PAELQKAVHD NLRNLGLDVL DVVNLRVMMG DGHGPAEGSI EASLTVLAEM 
       160        170        180        190        200
QQQGLVKHIG LSNVTPTQVA EARKIAEIVC VQNEYNIAHR ADDAMIDALA 
       210        220        230        240        250
HDGIAYVPFF PLGGFTPLQS STLSDVAASL GATPMQVALA WLLQRSPNIL 
       260        270        280 
LIPGTSSVAH LRENMAAEKL HLSEEVLSTL DGISRE
Length:286
Mass (Da):30,706
Last modified:May 1, 1992 - 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:i82B587AEA9115EF9
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
X62680 Genomic DNA Translation: CAA44553.1
U00096 Genomic DNA Translation: AAC74488.1
AP009048 Genomic DNA Translation: BAA15021.1
X97452 Genomic DNA Translation: CAA66103.1

Protein sequence database of the Protein Information Resource

More...PIRi		A48399

NCBI Reference Sequences

More...RefSeqi		NP_415924.1, NC_000913.3
WP_000097801.1, NZ_SSZK01000021.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74488; AAC74488; b1406
BAA15021; BAA15021; BAA15021

Database of genes from NCBI RefSeq genomes

More...GeneIDi		66674742
945980

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1403
eco:b1406

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.865

<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
X62680 Genomic DNA Translation: CAA44553.1
U00096 Genomic DNA Translation: AAC74488.1
AP009048 Genomic DNA Translation: BAA15021.1
X97452 Genomic DNA Translation: CAA66103.1
PIRiA48399
RefSeqiNP_415924.1, NC_000913.3
WP_000097801.1, NZ_SSZK01000021.1

3D structure databases

AlphaFoldDBiP25906
SMRiP25906
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4263019, 15 interactors
DIPiDIP-11632N
IntActiP25906, 4 interactors
STRINGi511145.b1406

2D gel databases

SWISS-2DPAGEiP25906

Proteomic databases

jPOSTiP25906
PaxDbiP25906
PRIDEiP25906

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		945980

Genome annotation databases

EnsemblBacteriaiAAC74488; AAC74488; b1406
BAA15021; BAA15021; BAA15021
GeneIDi66674742
945980
KEGGiecj:JW1403
eco:b1406
PATRICifig|1411691.4.peg.865

Organism-specific databases

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

More...EchoBASEi		EB1285

Phylogenomic databases

eggNOGiCOG0667, Bacteria
HOGENOMiCLU_023205_2_1_6
InParanoidiP25906
OMAiGYGTMQL
PhylomeDBiP25906

Enzyme and pathway databases

BioCyciEcoCyc:EG11309-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P25906

Family and domain databases

Gene3Di3.20.20.100, 1 hit
InterProiView protein in InterPro
IPR023210, NADP_OxRdtase_dom
IPR036812, NADP_OxRdtase_dom_sf
PfamiView protein in Pfam
PF00248, Aldo_ket_red, 1 hit
SUPFAMiSSF51430, SSF51430, 1 hit

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 nameiPDXI_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: P25906
<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: May 1, 1992
Last sequence update: May 1, 1992
Last modified: May 25, 2022
This is version 146 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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