PDX2_PLAF7
ID PDX2_PLAF7 Reviewed; 219 AA.
AC Q8IIK4; A0A143ZYM6; A0A144A0A4; Q5ND68;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 22-SEP-2009, sequence version 2.
DT 03-AUG-2022, entry version 96.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit PDX2 {ECO:0000303|PubMed:15590634};
DE Short=PfPDX2 {ECO:0000303|PubMed:15590634};
DE EC=4.3.3.6 {ECO:0000269|PubMed:16339145, ECO:0000269|PubMed:22244765};
DE AltName: Full=Pyridoxal 5'-phosphate synthase glutaminase subunit;
DE EC=3.5.1.2 {ECO:0000269|PubMed:15590634, ECO:0000269|PubMed:16339145, ECO:0000269|PubMed:22244765};
GN Name=PDX2 {ECO:0000303|PubMed:15590634}; ORFNames=PF11_0169, PF3D7_1116200;
OS Plasmodium falciparum (isolate 3D7).
OC Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC Plasmodiidae; Plasmodium; Plasmodium (Laverania).
OX NCBI_TaxID=36329;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, AND DEVELOPMENTAL
RP STAGE.
RC STRAIN=3D7;
RX PubMed=15590634; DOI=10.1074/jbc.m412475200;
RA Wrenger C., Eschbach M.L., Muller I.B., Warnecke D., Walter R.D.;
RT "Analysis of the vitamin B6 biosynthesis pathway in the human malaria
RT parasite Plasmodium falciparum.";
RL J. Biol. Chem. 280:5242-5248(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3D7;
RX PubMed=12368864; DOI=10.1038/nature01097;
RA Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W.,
RA Carlton J.M., Pain A., Nelson K.E., Bowman S., Paulsen I.T., James K.D.,
RA Eisen J.A., Rutherford K.M., Salzberg S.L., Craig A., Kyes S., Chan M.-S.,
RA Nene V., Shallom S.J., Suh B., Peterson J., Angiuoli S., Pertea M.,
RA Allen J., Selengut J., Haft D., Mather M.W., Vaidya A.B., Martin D.M.A.,
RA Fairlamb A.H., Fraunholz M.J., Roos D.S., Ralph S.A., McFadden G.I.,
RA Cummings L.M., Subramanian G.M., Mungall C., Venter J.C., Carucci D.J.,
RA Hoffman S.L., Newbold C., Davis R.W., Fraser C.M., Barrell B.G.;
RT "Genome sequence of the human malaria parasite Plasmodium falciparum.";
RL Nature 419:498-511(2002).
RN [3]
RP MUTAGENESIS OF GLU-53 AND ARG-154, AND SUBUNIT.
RC STRAIN=3D7;
RX PubMed=18350152; DOI=10.1371/journal.pone.0001815;
RA Mueller I.B., Knoeckel J., Groves M.R., Jordanova R., Ealick S.E.,
RA Walter R.D., Wrenger C.;
RT "The assembly of the plasmodial PLP synthase complex follows a defined
RT course.";
RL PLoS ONE 3:E1815-E1815(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP SUBCELLULAR LOCATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=3D7;
RX PubMed=16339145; DOI=10.1074/jbc.m508696200;
RA Gengenbacher M., Fitzpatrick T.B., Raschle T., Flicker K., Sinning I.,
RA Muller S., Macheroux P., Tews I., Kappes B.;
RT "Vitamin B6 biosynthesis by the malaria parasite Plasmodium falciparum:
RT biochemical and structural insights.";
RL J. Biol. Chem. 281:3633-3641(2006).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.61 ANGSTROMS) OF 3-219 OF MUTANT ASN-196 IN
RP COMPLEX WITH SUBUNIT PDX1 FROM P.BERGHEI, CATALYTIC ACTIVITY, SUBUNIT, AND
RP MUTAGENESIS OF HIS-196.
RC STRAIN=3D7;
RX PubMed=22244765; DOI=10.1016/j.str.2011.11.015;
RA Guedez G., Hipp K., Windeisen V., Derrer B., Gengenbacher M., Bottcher B.,
RA Sinning I., Kappes B., Tews I.;
RT "Assembly of the eukaryotic PLP-synthase complex from Plasmodium and
RT activation of the Pdx1 enzyme.";
RL Structure 20:172-184(2012).
CC -!- FUNCTION: Catalyzes the hydrolysis of glutamine to glutamate and
CC ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The
CC resulting ammonia molecule is channeled to the active site of Pdx1.
CC {ECO:0000269|PubMed:15590634, ECO:0000269|PubMed:16339145}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate +
CC L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-
CC phosphate; Xref=Rhea:RHEA:31507, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58273, ChEBI:CHEBI:58359, ChEBI:CHEBI:59776,
CC ChEBI:CHEBI:597326; EC=4.3.3.6;
CC Evidence={ECO:0000269|PubMed:16339145, ECO:0000269|PubMed:22244765};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-glutamine = L-glutamate + NH4(+);
CC Xref=Rhea:RHEA:15889, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:58359; EC=3.5.1.2;
CC Evidence={ECO:0000269|PubMed:15590634, ECO:0000269|PubMed:16339145,
CC ECO:0000269|PubMed:22244765};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.56 mM for L-glutamine {ECO:0000269|PubMed:16339145};
CC Note=kcat is 0.11 sec(-1) for L-glutamine.
CC {ECO:0000269|PubMed:16339145};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC -!- SUBUNIT: In the presence of Pdx1, forms a dodecamer of heterodimers.
CC Only shows activity in the heterodimer. {ECO:0000269|PubMed:18350152,
CC ECO:0000269|PubMed:22244765}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16339145}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8IIK4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8IIK4-2; Sequence=VSP_061284;
CC -!- DEVELOPMENTAL STAGE: Expressed throughout development. Highest
CC expression in segmenters stage followed by schizonts stage.
CC {ECO:0000269|PubMed:15590634}.
CC -!- SIMILARITY: Belongs to the glutaminase PdxT/SNO family. {ECO:0000305}.
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DR EMBL; AJ871406; CAI39217.1; -; mRNA.
DR EMBL; LN999945; CZT98822.1; -; Genomic_DNA.
DR EMBL; LN999945; CZT98823.1; -; Genomic_DNA.
DR RefSeq; XP_001347840.2; XM_001347804.2.
DR PDB; 2ABW; X-ray; 1.62 A; A/B=1-219.
DR PDB; 4ADS; X-ray; 3.61 A; G/H/I/J/K/L=3-219.
DR PDBsum; 2ABW; -.
DR PDBsum; 4ADS; -.
DR AlphaFoldDB; Q8IIK4; -.
DR SMR; Q8IIK4; -.
DR IntAct; Q8IIK4; 1.
DR STRING; 5833.PF11_0169; -.
DR MEROPS; C26.A35; -.
DR PRIDE; Q8IIK4; -.
DR EnsemblProtists; CZT98822; CZT98822; PF3D7_1116200.2. [Q8IIK4-2]
DR EnsemblProtists; CZT98823; CZT98823; PF3D7_1116200.1. [Q8IIK4-1]
DR GeneID; 810716; -.
DR KEGG; pfa:PF3D7_1116200.1; -.
DR VEuPathDB; PlasmoDB:PF3D7_1116200; -.
DR HOGENOM; CLU_069674_0_0_1; -.
DR InParanoid; Q8IIK4; -.
DR OMA; VFIRAPI; -.
DR OrthoDB; 1319510at2759; -.
DR PhylomeDB; Q8IIK4; -.
DR UniPathway; UPA00245; -.
DR Proteomes; UP000001450; Chromosome 11.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:1903600; C:glutaminase complex; IBA:GO_Central.
DR GO; GO:0004359; F:glutaminase activity; IDA:GeneDB.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008614; P:pyridoxine metabolic process; IBA:GO_Central.
DR GO; GO:0000304; P:response to singlet oxygen; IDA:GeneDB.
DR GO; GO:0042819; P:vitamin B6 biosynthetic process; IDA:GeneDB.
DR CDD; cd01749; GATase1_PB; 1.
DR Gene3D; 3.40.50.880; -; 1.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR002161; PdxT/SNO.
DR InterPro; IPR021196; PdxT/SNO_CS.
DR PANTHER; PTHR31559; PTHR31559; 1.
DR Pfam; PF01174; SNO; 1.
DR PIRSF; PIRSF005639; Glut_amidoT_SNO; 1.
DR SUPFAM; SSF52317; SSF52317; 1.
DR TIGRFAMs; TIGR03800; PLP_synth_Pdx2; 1.
DR PROSITE; PS01236; PDXT_SNO_1; 1.
DR PROSITE; PS51130; PDXT_SNO_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Glutamine amidotransferase;
KW Hydrolase; Lyase; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..219
FT /note="Pyridoxal 5'-phosphate synthase subunit PDX2"
FT /id="PRO_0000431778"
FT ACT_SITE 87
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT ACT_SITE 196
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT ACT_SITE 198
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT BINDING 52..54
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT BINDING 121
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT BINDING 153..154
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT VAR_SEQ 128..165
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_061284"
FT MUTAGEN 53
FT /note="E->Y: No glutaminase activity."
FT /evidence="ECO:0000269|PubMed:18350152"
FT MUTAGEN 154
FT /note="R->W: No glutaminase activity."
FT /evidence="ECO:0000269|PubMed:18350152"
FT MUTAGEN 196
FT /note="H->N: No activity."
FT /evidence="ECO:0000269|PubMed:22244765"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 16..23
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 38..42
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 54..60
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 63..77
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 83..86
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 88..92
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 94..98
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 107..109
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 115..120
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 130..134
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 149..154
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 157..161
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 167..174
FT /evidence="ECO:0007829|PDB:2ABW"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 178..187
FT /evidence="ECO:0007829|PDB:2ABW"
FT STRAND 190..195
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:2ABW"
FT HELIX 204..219
FT /evidence="ECO:0007829|PDB:2ABW"
SQ SEQUENCE 219 AA; 24563 MW; 21636561DFBCB136 CRC64;
MSEITIGVLS LQGDFEPHIN HFIKLQIPSL NIIQVRNVHD LGLCDGLVIP GGESTTVRRC
CAYENDTLYN ALVHFIHVLK KPIWGTCAGC ILLSKNVENI KLYSNFGNKF SFGGLDITIC
RNFYGSQNDS FICSLNIISD SSAFKKDLTA ACIRAPYIRE ILSDEVKVLA TFSHESYGPN
IIAAVEQNNC LGTVFHPELL PHTAFQQYFY EKVKNYKYS
