PDX1_DICDI
ID PDX1_DICDI Reviewed; 305 AA.
AC Q54J47;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Probable pyridoxal 5'-phosphate synthase subunit pdx1;
DE Short=PLP synthase subunit pdx1;
DE EC=4.3.3.6;
GN Name=pdx1; ORFNames=DDB_G0288299;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=AX2;
RX PubMed=16926386; DOI=10.1074/mcp.m600113-mcp200;
RA Gotthardt D., Blancheteau V., Bosserhoff A., Ruppert T., Delorenzi M.,
RA Soldati T.;
RT "Proteomics fingerprinting of phagosome maturation and evidence for the
RT role of a Galpha during uptake.";
RL Mol. Cell. Proteomics 5:2228-2243(2006).
CC -!- FUNCTION: Catalyzes the formation of pyridoxal 5'-phosphate from ribose
CC 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The
CC ammonia is provided by pdx2. Can also use ribulose 5-phosphate and
CC dihydroxyacetone phosphate as substrates, resulting from enzyme-
CC catalyzed isomerization of RBP and G3P, respectively.
CC {ECO:0000250|UniProtKB:Q03148}.
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:0000250|UniProtKB:Q03148};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC -!- SUBUNIT: Homohexamer. {ECO:0000250|UniProtKB:Q03148}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR EMBL; AAFI02000109; EAL63292.1; -; Genomic_DNA.
DR RefSeq; XP_636800.1; XM_631708.1.
DR AlphaFoldDB; Q54J47; -.
DR SMR; Q54J47; -.
DR STRING; 44689.DDB0237963; -.
DR PaxDb; Q54J47; -.
DR EnsemblProtists; EAL63292; EAL63292; DDB_G0288299.
DR GeneID; 8626557; -.
DR KEGG; ddi:DDB_G0288299; -.
DR dictyBase; DDB_G0288299; pdx1.
DR eggNOG; KOG1606; Eukaryota.
DR HOGENOM; CLU_055352_1_0_1; -.
DR InParanoid; Q54J47; -.
DR OMA; RYANRGW; -.
DR PhylomeDB; Q54J47; -.
DR UniPathway; UPA00245; -.
DR PRO; PR:Q54J47; -.
DR Proteomes; UP000002195; Chromosome 5.
DR GO; GO:0045335; C:phagocytic vesicle; HDA:dictyBase.
DR GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
DR GO; GO:0008614; P:pyridoxine metabolic process; ISS:dictyBase.
DR CDD; cd04727; pdxS; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01824; PdxS; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001852; PdxS/SNZ.
DR InterPro; IPR033755; PdxS/SNZ_N.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR31829; PTHR31829; 1.
DR Pfam; PF01680; SOR_SNZ; 1.
DR PIRSF; PIRSF029271; Pdx1; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR00343; TIGR00343; 1.
DR PROSITE; PS01235; PDXS_SNZ_1; 1.
DR PROSITE; PS51129; PDXS_SNZ_2; 1.
PE 1: Evidence at protein level;
KW Lyase; Pyridoxal phosphate; Reference proteome; Schiff base.
FT CHAIN 1..305
FT /note="Probable pyridoxal 5'-phosphate synthase subunit
FT pdx1"
FT /id="PRO_0000328202"
FT ACT_SITE 90
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 33
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 162
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 174
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:Q03148"
FT BINDING 223
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 244..245
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
SQ SEQUENCE 305 AA; 33137 MW; 8790E7B1D04D77CF CRC64;
MENLTENQAT NNNSPFRIKS SLAQMLKGGV IMDVVTPEQA RIAEEAGACA VMALEKIPAD
IRHFGGVARM SDPGMIKEIM NAVTIPVMAK VRIGHFVEAQ ILQEIGVDYI DESEVLTIAD
NENHIDKSEF KVPFVCGCRN LGEALRRISE GAAMIRTKGE AGTGDVVEAV RHARAVNKEI
KKIQNMDPHE LYTYAKEIQA PLELVKEVKR LGRLPVVNFA AGGVATPADA AMMMQLGMDG
VFVGSGIFKS GDPAKRAKAI VQAVTHFNNP QIVAKVSENL GEAMVGINVD TLKDKENQNW
STKEK
