Q8L940 (PDX13_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pyridoxal biosynthesis protein PDX1.3
Short name=AtPDX1.3
Short name=AtPDX1;1

Gene names

Name:	PDX13
Synonyms:	GIP2, PDX1L3, RSR4
Ordered Locus Names:	At5g01410
ORF Names:	T10O8.120

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	309 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in the production of pyridoxal (vitamin B6). Also plays an indirect role in osmotic or salt tolerance, and in resistance to singlet oxygen-generating photosensitizers. Ref.1 Ref.8
Pathway	Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
Subunit structure	Homodimer or heterodimer with PDX1.1 or PDX1.2. Interacts with PDX2. Ref.2
Subcellular location	Cytoplasm. Cell membrane. Membrane Ref.1 Ref.8.
Tissue specificity	Expressed in cotyledons, rapidly dividing root stele tissues, stems, leaves, flowers, mature pollen, and siliques. Ref.1 Ref.2
Induction	Not induced by cold, salt, drought or UV stress, or by abscisic acid or jasmonic acid. Ref.1
Post-translational modification	Ubiquitinated. Ref.9
Disruption phenotype	Plants have a lower leaf carotenoid and chlorophyll a and b content, and are impaired both in root cell division and in root cell elongation. Mutant rsr4-1 can be complemented by the addition of any of the vitamin B6 vitamers, except pyridoxal 5'-phosphate. Ref.1
Miscellaneous	In plants, synthesis of vitamin B6 does not involve deoxyxylulose 5-phosphate but utilizes intermediates from the pentose phosphate pathway and from glycolysis. Vitamin B6 is an essential quencher of singlet oxygen in plants, that can protect cellular membranes from lipid peroxidation.
Sequence similarities	Belongs to the pdxS/SNZ family.

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Cellular component	Cell membrane Cytoplasm Membrane
PTM	Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cellular amino acid metabolic process Inferred from mutant phenotype Ref.2. Source: TAIR chlorophyll metabolic process Inferred from mutant phenotype Ref.2. Source: TAIR hyperosmotic salinity response Inferred from mutant phenotype Ref.1. Source: TAIR pyridoxal phosphate biosynthetic process Inferred from electronic annotation. Source: InterPro pyridoxine biosynthetic process Inferred from genetic interaction Ref.1. Source: TAIR response to lipid hydroperoxide Inferred from mutant phenotype Ref.1. Source: TAIR response to non-ionic osmotic stress Inferred from mutant phenotype. Source: TAIR
Cellular component	cytosol Inferred from direct assay Ref.8. Source: TAIR endomembrane system Inferred from direct assay Ref.1. Source: TAIR plasma membrane Inferred from direct assay Ref.1. Source: TAIR
Molecular function	catalytic activity Inferred from electronic annotation. Source: InterPro protein homodimerization activity Inferred from physical interaction Ref.2. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PDX12	Q9ZNR6	5	EBI-1545956,EBI-1545987

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 309	309	Pyridoxal biosynthesis protein PDX1.3		PRO_0000109368
Experimental info
	Mutagenesis	54	1	G → S in rsr4-1; strongly reduced oligomerization and 63% reduction in pyridoxal biosynthesis. Ref.2
	Sequence conflict	226	1	F → S in AAM66972. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	Q8L940 [UniParc]. Last modified March 15, 2004. Version 2. Checksum: E74EBBCD4F124456	FASTA	309	33,216
	10 20 30 40 50 60 MEGTGVVAVY GNGAITEAKK SPFSVKVGLA QMLRGGVIMD VVNAEQARIA EEAGACAVMA 70 80 90 100 110 120 LERVPADIRA QGGVARMSDP QMIKEIKQAV TIPVMAKARI GHFVEAQILE AIGIDYIDES 130 140 150 160 170 180 EVLTLADEDH HINKHNFRIP FVCGCRNLGE ALRRIREGAA MIRTKGEAGT GNIIEAVRHV 190 200 210 220 230 240 RSVNGDIRVL RNMDDDEVFT FAKKLAAPYD LVMQTKQLGR LPVVQFAAGG VATPADAALM 250 260 270 280 290 300 MQLGCDGVFV GSGIFKSGDP ARRARAIVQA VTHYSDPEML VEVSCGLGEA MVGINLNDEK VERFANRSE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Pyridoxine is required for post-embryonic root development and tolerance to osmotic and oxidative stresses." Chen H., Xiong L. Plant J. 44:396-408(2005) [PubMed: 16236150] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY, INDUCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[2]	"Analysis of the Arabidopsis rsr4-1/pdx1-3 mutant reveals the critical function of the PDX1 protein family in metabolism, development, and vitamin B6 biosynthesis." Wagner S., Bernhardt A., Leuendorf J.E., Drewke C., Lytovchenko A., Mujahed N., Gurgui C., Frommer W.B., Leistner E., Fernie A.R., Hellmann H. Plant Cell 18:1722-1735(2006) [PubMed: 16766694] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-54, TISSUE SPECIFICITY, INTERACTION WITH PDX1.1; PDX1.2 AND PDX2. Strain: cv. C24.
[3]	"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana." Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F. Nature 408:823-826(2000) [PubMed: 11130714] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[5]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[6]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[7]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[8]	"Vitamin B6 biosynthesis in higher plants." Tambasco-Studart M., Titiz O., Raschle T., Forster G., Amrhein N., Fitzpatrick T.B. Proc. Natl. Acad. Sci. U.S.A. 102:13687-13692(2005) [PubMed: 16157873] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[9]	"Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis." Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D. Plant J. 59:344-358(2009) [PubMed: 19292762] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY972813 mRNA. Translation: AAY42123.1. AL161746 Genomic DNA. Translation: CAB81924.1. CP002688 Genomic DNA. Translation: AED90340.1. AF428298 mRNA. Translation: AAL16130.1. AF446352 mRNA. Translation: AAL48227.1. AY097428 mRNA. Translation: AAM19944.1. AY088650 mRNA. Translation: AAM66972.1. AK227197 mRNA. Translation: BAE99236.1.
IPI	IPI00544908.
PIR	T48163.
RefSeq	NP_195761.1. NM_120219.1.
UniGene	At.23386.
3D structure databases
ProteinModelPortal	Q8L940.
SMR	Q8L940. Positions 23-291.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8L940. 4 interactions.
STRING	Q8L940.
Proteomic databases
PRIDE	Q8L940.
ProMEX	Q8L940.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT5G01410.1; AT5G01410.1; AT5G01410.
GeneID	831738.
GenomeReviews	Gene locus AT5G01410 in contig BA000015_GR.
KEGG	ath:AT5G01410.
NMPDR	fig|3702.1.peg.22207.
Organism-specific databases
TAIR	At5g01410.
Phylogenomic databases
eggNOG	KOG1606.
GeneTree	EPGT00050000010473.
HOGENOM	HBG292342.
InParanoid	Q8L940.
OMA	RIWEGAA.
PhylomeDB	Q8L940.
ProtClustDB	CLSN2683112.
Gene expression databases
ArrayExpress	Q8L940.
Genevestigator	Q8L940.
GermOnline	AT5G01410. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR013785. Aldolase_TIM. IPR011060. RibuloseP-bd_barrel. IPR001852. Snz1p/Sor1. [Graphical view]
Gene3D	G3DSA:3.20.20.70. Aldolase_TIM. 2 hits.
KO	K06215.
PANTHER	PTHR22854:SF9. PTHR22854:SF9. 1 hit.
Pfam	PF01680. SOR_SNZ. 1 hit. [Graphical view]
PIRSF	PIRSF029271. Pdx1. 1 hit.
SUPFAM	SSF51366. RibP_bind_barrel. 1 hit.
TIGRFAMs	TIGR00343. TIGR00343. 1 hit.
PROSITE	PS01235. PDXS_SNZ_1. 1 hit. PS51129. PDXS_SNZ_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PDX13_ARATH

Accession

Primary (citable) accession number: Q8L940
Secondary accession number(s): Q3KRU4, Q9M032

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2004
Last sequence update:	March 15, 2004
Last modified:	December 14, 2011
This is version 75 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program