Reviewed, UniProtKB/Swiss-Prot Q8L940 (PDX13_ARATH)

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) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	309 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.7
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.7
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
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
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	amino acid metabolic process Ref.2 Inferred from mutant phenotype. Source: TAIR chlorophyll metabolic process Ref.2 Inferred from mutant phenotype. Source: TAIR hyperosmotic salinity response Ref.1 Inferred from mutant phenotype. Source: TAIR pyridoxine biosynthetic process Ref.1 Inferred from genetic interaction. Source: TAIR response to UV-B Inferred from genetic interaction. Source: TAIR response to lipid hydroperoxide Ref.1 Inferred from mutant phenotype. Source: TAIR response to non-ionic osmotic stress Inferred from mutant phenotype. Source: TAIR
Cellular component	cytosol Ref.7 Inferred from direct assay. Source: TAIR endomembrane system Ref.1 Inferred from direct assay. Source: TAIR plasma membrane Ref.1 Inferred from direct assay. Source: TAIR
Molecular function	catalytic activity Inferred from electronic annotation. Source: InterPro protein heterodimerization activity Ref.2 Inferred from physical interaction. Source: TAIR protein homodimerization activity Ref.2 Inferred from physical interaction. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PDX12	Q9ZNR6	1	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.5

Sequences

	Sequence		Length	Mass (Da)
	Q8L940-1 [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]	"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.
[5]	"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].
[6]	"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.
[7]	"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.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AY972813 mRNA. Translation: AAY42123.1. AL161746 Genomic DNA. Translation: CAB81924.1. 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.
UniGene	At.23386
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8L940. 4 interactions.
Proteomic databases
PRIDE	Q8L940.
ProMEX	Q8L940.
Genome annotation databases
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
OMA	Q8L940. ARMSDPD.
Gene expression databases
ArrayExpress	Q8L940.
GermOnline	AT5G01410. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001852. Snz1p/Sor1. [Graphical view]
Pfam	PF01680. SOR_SNZ. 1 hit. [Graphical view]
PIRSF	PIRSF029271. Pdx1. 1 hit.
ProDom	PD004958. Snz1p/Sor1. 1 hit. [Graphical view] [Entries sharing at least one domain]
TIGRFAMs	TIGR00343. Snz1p/Sor1. 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:	June 16, 2009
This is version 52 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)