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UniProtKB - Q9ZNR6 (PDX12_ARATH)

Entry version 137 (18 Sep 2019)
Sequence version 1 (01 May 1999)
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Protein

Pyridoxal 5'-phosphate synthase-like subunit PDX1.2

Gene

PDX12

Organism
Arabidopsis thaliana (Mouse-ear cress)
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

The protein has no function in the formation of pyridoxal 5'-phosphate.1 Publication

Miscellaneous

Unlike PDX1.1 or PDX1.3, PDX1.2 is unable to interact with PDX2 and restore prototrophy in yeast snz1 mutants.

<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

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

LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		ARA:GQT-784-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_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:
Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
Short name:
AtPDX1.2
Short name:
AtPDX1;3
<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:PDX12
Synonyms:A37, PDX1L2
Ordered Locus Names:At3g16050
ORF Names:MSL1.3
<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>OrganismiArabidopsis thaliana (Mouse-ear cress)
<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 identifieri3702 [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 lineageiEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliopsida › eudicotyledons › Gunneridae › Pentapetalae › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis
<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
  • UP000006548 <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

Organism-specific databases

Arabidopsis Information Portal

More...Araporti		AT3G16050

The Arabidopsis Information Resource

More...TAIRi		locus:2093427 AT3G16050

<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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

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 <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 methionineiRemovedCombined sources
<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_00001093672 – 314Pyridoxal 5'-phosphate synthase-like subunit PDX1.2Add BLAST313

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylalanineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

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

More...PaxDbi		Q9ZNR6

PRoteomics IDEntifications database

More...PRIDEi		Q9ZNR6

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		Q9ZNR6

<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 provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Expressed in callus tissues, flowers and roots. Weakly expressed in leaves and stems.2 Publications

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		Q9ZNR6 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		Q9ZNR6 AT

<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 or heterodimer with PDX1.1 or PDX1.3. No interaction with PDX2.

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
Q8L9405EBI-1545987,EBI-1545956

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		6184, 5 interactors

Protein interaction database and analysis system

More...IntActi		Q9ZNR6, 2 interactors

STRING: functional protein association networks

More...STRINGi		3702.AT3G16050.1

<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

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

More...SMRi		Q9ZNR6

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		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 PdxS/SNZ family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG1606 Eukaryota
COG0214 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000227586

KEGG Orthology (KO)

More...KOi		K06215

Identification of Orthologs from Complete Genome Data

More...OMAi		NKHNFRA

Database of Orthologous Groups

More...OrthoDBi		1090029at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q9ZNR6

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.20.20.70, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR013785 Aldolase_TIM
IPR001852 PdxS/SNZ
IPR033755 PdxS/SNZ_N
IPR011060 RibuloseP-bd_barrel

The PANTHER Classification System

More...PANTHERi		PTHR31829 PTHR31829, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01680 SOR_SNZ, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF029271 Pdx1, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF51366 SSF51366, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01235 PDXS_SNZ_1, 1 hit
PS51129 PDXS_SNZ_2, 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.

Q9ZNR6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MADQAMTDQD QGAVTLYSGT AITDAKKNHP FSVKVGLAQV LRGGAIVEVS 
        60         70         80         90        100
SVNQAKLAES AGACSVIVSD PVRSRGGVRR MPDPVLIKEV KRAVSVPVMA 
       110        120        130        140        150
RARVGHFVEA QILESLAVDY IDESEIISVA DDDHFINKHN FRSPFICGCR 
       160        170        180        190        200
DTGEALRRIR EGAAMIRIQG DLTATGNIAE TVKNVRSLMG EVRVLNNMDD 
       210        220        230        240        250
DEVFTFAKKI SAPYDLVAQT KQMGRVPVVQ FASGGITTPA DAALMMQLGC 
       260        270        280        290        300
DGVFVGSEVF DGPDPFKKLR SIVQAVQHYN DPHVLAEMSS GLENAMESLN 
       310 
VRGDRIQDFG QGSV
Length:314
Mass (Da):33,836
Last modified:May 1, 1999 - 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:iD894BC393CBBBA6A
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
AF029980 mRNA Translation: AAD01897.1
AF029981 Genomic DNA Translation: AAD01898.1
AB012247 Genomic DNA Translation: BAB02670.1
CP002686 Genomic DNA Translation: AEE75766.1
BT003136 mRNA Translation: AAO24568.1
AK228092 mRNA Translation: BAF00051.1

NCBI Reference Sequences

More...RefSeqi		NP_188226.1, NM_112475.3

Genome annotation databases

Ensembl plant genome annotation project

More...EnsemblPlantsi		AT3G16050.1; AT3G16050.1; AT3G16050

Database of genes from NCBI RefSeq genomes

More...GeneIDi		820850

Gramene; a comparative resource for plants

More...Gramenei		AT3G16050.1; AT3G16050.1; AT3G16050

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ath:AT3G16050

<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
AF029980 mRNA Translation: AAD01897.1
AF029981 Genomic DNA Translation: AAD01898.1
AB012247 Genomic DNA Translation: BAB02670.1
CP002686 Genomic DNA Translation: AEE75766.1
BT003136 mRNA Translation: AAO24568.1
AK228092 mRNA Translation: BAF00051.1
RefSeqiNP_188226.1, NM_112475.3

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
6HX3X-ray2.00A/C/E/G1-314[»]
6HXGX-ray1.90A/C/E/G1-314[»]
6HYEX-ray2.53A/C/E/G1-314[»]
SMRiQ9ZNR6
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi6184, 5 interactors
IntActiQ9ZNR6, 2 interactors
STRINGi3702.AT3G16050.1

PTM databases

iPTMnetiQ9ZNR6

Proteomic databases

PaxDbiQ9ZNR6
PRIDEiQ9ZNR6

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		820850

Genome annotation databases

EnsemblPlantsiAT3G16050.1; AT3G16050.1; AT3G16050
GeneIDi820850
GrameneiAT3G16050.1; AT3G16050.1; AT3G16050
KEGGiath:AT3G16050

Organism-specific databases

AraportiAT3G16050
TAIRilocus:2093427 AT3G16050

Phylogenomic databases

eggNOGiKOG1606 Eukaryota
COG0214 LUCA
HOGENOMiHOG000227586
KOiK06215
OMAiNKHNFRA
OrthoDBi1090029at2759
PhylomeDBiQ9ZNR6

Enzyme and pathway databases

BioCyciARA:GQT-784-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q9ZNR6

Gene expression databases

ExpressionAtlasiQ9ZNR6 baseline and differential
GenevisibleiQ9ZNR6 AT

Family and domain databases

Gene3Di3.20.20.70, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR001852 PdxS/SNZ
IPR033755 PdxS/SNZ_N
IPR011060 RibuloseP-bd_barrel
PANTHERiPTHR31829 PTHR31829, 1 hit
PfamiView protein in Pfam
PF01680 SOR_SNZ, 1 hit
PIRSFiPIRSF029271 Pdx1, 1 hit
SUPFAMiSSF51366 SSF51366, 1 hit
PROSITEiView protein in PROSITE
PS01235 PDXS_SNZ_1, 1 hit
PS51129 PDXS_SNZ_2, 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 nameiPDX12_ARATH
<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: Q9ZNR6
Secondary accession number(s): Q0WS48
<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: March 15, 2004
Last sequence update: May 1, 1999
Last modified: September 18, 2019
This is version 137 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 programPlant 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. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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