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Probable pyridoxal 5'-phosphate synthase subunit PDX2 (AtPDX2) (EC 4.3.3.6) (Protein EMBRYO DEFECTIVE 2407) (Pyridoxal 5'-phosphate synthase glutaminase subunit) (EC 3.5.1.2)

 PDX2_ARATH              Reviewed;         255 AA.
Q8LAD0; Q56ZP9; Q9FKJ3;
09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
01-OCT-2002, sequence version 1.
25-APR-2018, entry version 100.
RecName: Full=Probable pyridoxal 5'-phosphate synthase subunit PDX2;
Short=AtPDX2;
EC=4.3.3.6 {ECO:0000269|PubMed:17468224};
AltName: Full=Protein EMBRYO DEFECTIVE 2407;
AltName: Full=Pyridoxal 5'-phosphate synthase glutaminase subunit;
EC=3.5.1.2 {ECO:0000269|PubMed:17468224};
Name=PDX2; Synonyms=EMB2407; OrderedLocusNames=At5g60540;
ORFNames=muf9.190;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=9679202; DOI=10.1093/dnares/5.2.131;
Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
features of the regions of 1,381,565 bp covered by twenty one
physically assigned P1 and TAC clones.";
DNA Res. 5:131-145(1998).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=11910074; DOI=10.1126/science.1071006;
Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
Shibata K., Shinagawa A., Shinozaki K.;
"Functional annotation of a full-length Arabidopsis cDNA collection.";
Science 296:141-145(2002).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
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.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 211-255.
STRAIN=cv. Columbia;
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.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
[7]
FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=16157873; DOI=10.1073/pnas.0506228102;
Tambasco-Studart M., Titiz O., Raschle T., Forster G., Amrhein N.,
Fitzpatrick T.B.;
"Vitamin B6 biosynthesis in higher plants.";
Proc. Natl. Acad. Sci. U.S.A. 102:13687-13692(2005).
[8]
TISSUE SPECIFICITY, AND INTERACTION WITH PDX1.1 AND PDX1.3.
STRAIN=cv. C24;
PubMed=16766694; DOI=10.1105/tpc.105.036269;
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.;
"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.";
Plant Cell 18:1722-1735(2006).
[9]
FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=17468224; DOI=10.1104/pp.107.096784;
Tambasco-Studart M., Tews I., Amrhein N., Fitzpatrick T.B.;
"Functional analysis of PDX2 from Arabidopsis, a glutaminase involved
in vitamin B6 biosynthesis.";
Plant Physiol. 144:915-925(2007).
[10]
INTERACTION WITH RPA2A.
PubMed=20706207; DOI=10.1038/msb.2010.53;
Van Leene J., Hollunder J., Eeckhout D., Persiau G., Van De Slijke E.,
Stals H., Van Isterdael G., Verkest A., Neirynck S., Buffel Y.,
De Bodt S., Maere S., Laukens K., Pharazyn A., Ferreira P.C.G.,
Eloy N., Renne C., Meyer C., Faure J.-D., Steinbrenner J., Beynon J.,
Larkin J.C., Van de Peer Y., Hilson P., Kuiper M., De Veylder L.,
Van Onckelen H., Inze D., Witters E., De Jaeger G.;
"Targeted interactomics reveals a complex core cell cycle machinery in
Arabidopsis thaliana.";
Mol. Syst. Biol. 6:397-397(2010).
-!- FUNCTION: Catalyzes the hydrolysis of glutamine to glutamate and
ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The
resulting ammonia molecule is channeled to the active site of
PDX1. Involved in the indirect resistance to singlet oxygen-
generating photosensitizers. {ECO:0000269|PubMed:16157873,
ECO:0000269|PubMed:17468224}.
-!- CATALYTIC ACTIVITY: D-ribose 5-phosphate + D-glyceraldehyde 3-
phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3
H(2)O + phosphate. {ECO:0000269|PubMed:17468224}.
-!- CATALYTIC ACTIVITY: L-glutamine + H(2)O = L-glutamate + NH(3).
{ECO:0000269|PubMed:17468224}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.92 mM for L-glutamine {ECO:0000269|PubMed:16157873};
Note=kcat is 0.023 min(-1) for L-glutamine.
{ECO:0000269|PubMed:16157873};
-!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate
biosynthesis.
-!- SUBUNIT: Interacts with PDX1.1 or PDX1.3, but not with PDX1.2.
Binds to RPA2A. {ECO:0000269|PubMed:16766694,
ECO:0000269|PubMed:20706207}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16157873}.
-!- TISSUE SPECIFICITY: Strongly expressed in roots, stems, leaves and
flowers. {ECO:0000269|PubMed:16766694}.
-!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous.
{ECO:0000269|PubMed:16157873}.
-!- MISCELLANEOUS: In plants, synthesis of vitamin B6 does not involve
deoxyxylulose 5-phosphate but utilizes intermediates from the
pentose phosphate pathway and from glycolysis.
-!- MISCELLANEOUS: Vitamin B6 is an essential quencher of singlet
oxygen in plants, that can protect cellular membranes from lipid
peroxidation.
-!- SIMILARITY: Belongs to the glutaminase PdxT/SNO family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAB08237.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=BAD94363.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AB011483; BAB08237.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002688; AED97341.1; -; Genomic_DNA.
EMBL; AK117313; BAC41984.1; -; mRNA.
EMBL; BT005266; AAO63330.1; -; mRNA.
EMBL; AY087902; AAM65453.1; -; mRNA.
EMBL; AK220914; BAD94363.1; ALT_INIT; mRNA.
RefSeq; NP_568922.1; NM_125447.2.
UniGene; At.29154; -.
ProteinModelPortal; Q8LAD0; -.
SMR; Q8LAD0; -.
BioGrid; 21419; 6.
IntAct; Q8LAD0; 5.
STRING; 3702.AT5G60540.1; -.
MEROPS; C26.A32; -.
PaxDb; Q8LAD0; -.
PRIDE; Q8LAD0; -.
EnsemblPlants; AT5G60540.1; AT5G60540.1; AT5G60540.
GeneID; 836175; -.
Gramene; AT5G60540.1; AT5G60540.1; AT5G60540.
KEGG; ath:AT5G60540; -.
Araport; AT5G60540; -.
TAIR; locus:2175083; AT5G60540.
eggNOG; KOG3210; Eukaryota.
eggNOG; COG0311; LUCA.
HOGENOM; HOG000039949; -.
InParanoid; Q8LAD0; -.
KO; K08681; -.
OMA; VFIRAPI; -.
OrthoDB; EOG09360JS7; -.
PhylomeDB; Q8LAD0; -.
BioCyc; ARA:AT5G60540-MONOMER; -.
BioCyc; MetaCyc:AT5G60540-MONOMER; -.
UniPathway; UPA00245; -.
PRO; PR:Q8LAD0; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q8LAD0; baseline and differential.
Genevisible; Q8LAD0; AT.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:1903600; C:glutaminase complex; IBA:GO_Central.
GO; GO:0004359; F:glutaminase activity; IDA:TAIR.
GO; GO:0046982; F:protein heterodimerization activity; IPI:TAIR.
GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-KW.
GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
GO; GO:0008614; P:pyridoxine metabolic process; IBA:GO_Central.
GO; GO:0042819; P:vitamin B6 biosynthetic process; IMP:TAIR.
CDD; cd01749; GATase1_PB; 1.
Gene3D; 3.40.50.880; -; 1.
HAMAP; MF_01615; PdxT; 1.
InterPro; IPR029062; Class_I_gatase-like.
InterPro; IPR002161; PdxT/SNO.
InterPro; IPR021196; PdxT/SNO_CS.
PANTHER; PTHR31559; PTHR31559; 1.
Pfam; PF01174; SNO; 1.
PIRSF; PIRSF005639; Glut_amidoT_SNO; 1.
SUPFAM; SSF52317; SSF52317; 1.
TIGRFAMs; TIGR03800; PLP_synth_Pdx2; 1.
PROSITE; PS01236; PDXT_SNO_1; 1.
PROSITE; PS51130; PDXT_SNO_2; 1.
1: Evidence at protein level;
Complete proteome; Cytoplasm; Glutamine amidotransferase; Hydrolase;
Lyase; Pyridoxal phosphate; Reference proteome.
CHAIN 1 255 Probable pyridoxal 5'-phosphate synthase
subunit PDX2.
/FTId=PRO_0000270626.
REGION 46 48 L-glutamine binding.
{ECO:0000250|UniProtKB:P37528}.
REGION 142 143 L-glutamine binding.
{ECO:0000250|UniProtKB:P37528}.
COMPBIAS 227 231 Poly-Ser.
ACT_SITE 78 78 Nucleophile.
{ECO:0000250|UniProtKB:P37528}.
ACT_SITE 202 202 Charge relay system.
{ECO:0000250|UniProtKB:P37528}.
ACT_SITE 204 204 Charge relay system.
{ECO:0000250|UniProtKB:P37528}.
BINDING 108 108 L-glutamine.
{ECO:0000250|UniProtKB:P37528}.
CONFLICT 212 212 H -> P (in Ref. 6; BAD94363).
{ECO:0000305}.
SEQUENCE 255 AA; 27438 MW; 2B6447833990A677 CRC64;
MTVGVLALQG SFNEHIAALR RLGVQGVEIR KADQLLTVSS LIIPGGESTT MAKLAEYHNL
FPALREFVKM GKPVWGTCAG LIFLADRAVG QKEGGQELVG GLDCTVHRNF FGSQIQSFEA
DILVPQLTSQ EGGPETYRGV FIRAPAVLDV GPDVEVLADY PVPSNKVLYS SSTVQIQEED
ALPETKVIVA VKQGNLLATA FHPELTADTR WHSYFIKMTK EIEQGASSSS SKTIVSVGET
SAGPEPAKPD LPIFQ


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