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Pyridoxine 5'-phosphate synthase (PNP synthase) (EC 2.6.99.2)

 PDXJ_ECOLI              Reviewed;         243 AA.
P0A794; P24223; Q2MAG6;
07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
28-MAR-2018, entry version 113.
RecName: Full=Pyridoxine 5'-phosphate synthase;
Short=PNP synthase;
EC=2.6.99.2;
Name=pdxJ; OrderedLocusNames=b2564, JW2548;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
STRAIN=K12;
PubMed=1537799; DOI=10.1128/jb.174.5.1544-1553.1992;
Takiff H.E., Baker T., Copeland T., Chen S.-M., Court D.L.;
"Locating essential Escherichia coli genes by using mini-Tn10
transposons: the pdxJ operon.";
J. Bacteriol. 174:1544-1553(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=1537800; DOI=10.1128/jb.174.5.1554-1567.1992;
Lam H.-M., Tancula E., Dempsey W.B., Winkler M.E.;
"Suppression of insertions in the complex pdxJ operon of Escherichia
coli K-12 by lon and other mutations.";
J. Bacteriol. 174:1554-1567(1992).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
Nashimoto H., Saito N.;
Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
VARIANT SER-194.
PubMed=8636054; DOI=10.1128/jb.178.8.2445-2449.1996;
Man T.K., Zhao G., Winkler M.E.;
"Isolation of a pdxJ point mutation that bypasses the requirement for
the PdxH oxidase in pyridoxal 5'-phosphate coenzyme biosynthesis in
Escherichia coli K-12.";
J. Bacteriol. 178:2445-2449(1996).
[7]
FUNCTION.
STRAIN=K12 / ATCC 35607 / JM83;
PubMed=10225425; DOI=10.1016/S0014-5793(99)00393-2;
Laber B., Maurer W., Scharf S., Stepusin K., Schmidt F.S.;
"Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-
(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by
PdxA and PdxJ protein.";
FEBS Lett. 449:45-48(1999).
[8]
CRYSTALLIZATION.
PubMed=10944349; DOI=10.1107/S0907444900007368;
Garrido Franco M., Huber R., Schmidt F.S., Laber B., Clausen T.;
"Crystallization and preliminary X-ray crystallographic analysis of
PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme.";
Acta Crystallogr. D 56:1045-1048(2000).
[9]
REVIEW.
PubMed=12686115; DOI=10.1016/S1570-9639(03)00065-7;
Garrido-Franco M.;
"Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and
beyond.";
Biochim. Biophys. Acta 1647:92-97(2003).
[10]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PRODUCT, AND
SUBUNIT.
PubMed=11286891; DOI=10.1016/S0969-2126(01)00584-6;
Garrido Franco M., Laber B., Huber R., Clausen T.;
"Structural basis for the function of pyridoxine 5'-phosphate
synthase.";
Structure 9:245-253(2001).
[11]
X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF APOENZYME AND COMPLEX WITH
SUBSTRATE, AND SUBUNIT.
PubMed=12269807; DOI=10.1021/bi026292t;
Yeh J.I., Du S., Pohl E., Cane D.E.;
"Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A
crystal structure in complex with 1-deoxy-D-xylulose phosphate.";
Biochemistry 41:11649-11657(2002).
[12]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE AND
SUBSTRATE ANALOG, AND REACTION MECHANISM.
PubMed=12206776; DOI=10.1016/S0022-2836(02)00695-2;
Garrido-Franco M., Laber B., Huber R., Clausen T.;
"Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase:
implications for substrate binding and catalysis.";
J. Mol. Biol. 321:601-612(2002).
-!- FUNCTION: Catalyzes the complicated ring closure reaction between
the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and
3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP)
to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate.
{ECO:0000269|PubMed:10225425}.
-!- CATALYTIC ACTIVITY: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-
oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2
H(2)O.
-!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate
biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-
phosphate: step 5/5.
-!- SUBUNIT: Homooctamer; tetramer of dimers.
{ECO:0000269|PubMed:11286891, ECO:0000269|PubMed:12269807}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- SIMILARITY: Belongs to the PNP synthase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=D64044; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; M76470; AAA21845.1; -; Genomic_DNA.
EMBL; M74526; AAA24315.1; -; Genomic_DNA.
EMBL; D64044; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; U36841; AAA79826.1; -; Genomic_DNA.
EMBL; U00096; AAC75617.1; -; Genomic_DNA.
EMBL; AP009048; BAE76740.1; -; Genomic_DNA.
PIR; A42293; A42293.
RefSeq; NP_417059.1; NC_000913.3.
RefSeq; WP_001297412.1; NZ_LN832404.1.
PDB; 1HO1; X-ray; 2.00 A; A/B/C/D=2-243.
PDB; 1HO4; X-ray; 2.30 A; A/B/C/D=2-243.
PDB; 1IXN; X-ray; 2.30 A; A/B/C/D=2-243.
PDB; 1IXO; X-ray; 2.30 A; A/B/C/D=2-243.
PDB; 1IXP; X-ray; 2.30 A; A/B/C/D=2-243.
PDB; 1IXQ; X-ray; 2.30 A; A/B/C/D=2-243.
PDB; 1M5W; X-ray; 1.96 A; A/B/C/D/E/F/G/H=1-243.
PDBsum; 1HO1; -.
PDBsum; 1HO4; -.
PDBsum; 1IXN; -.
PDBsum; 1IXO; -.
PDBsum; 1IXP; -.
PDBsum; 1IXQ; -.
PDBsum; 1M5W; -.
ProteinModelPortal; P0A794; -.
SMR; P0A794; -.
BioGrid; 4260601; 32.
DIP; DIP-36215N; -.
IntAct; P0A794; 5.
STRING; 316385.ECDH10B_2732; -.
DrugBank; DB02496; 1-Deoxy-D-xylulose 5-phosphate.
DrugBank; DB02515; 3-Phosphoglycerol.
DrugBank; DB02209; Pyridoxine-5'-Phosphate.
EPD; P0A794; -.
PaxDb; P0A794; -.
PRIDE; P0A794; -.
EnsemblBacteria; AAC75617; AAC75617; b2564.
EnsemblBacteria; BAE76740; BAE76740; BAE76740.
GeneID; 947039; -.
KEGG; ecj:JW2548; -.
KEGG; eco:b2564; -.
PATRIC; fig|1411691.4.peg.4170; -.
EchoBASE; EB0687; -.
EcoGene; EG10693; pdxJ.
eggNOG; ENOG4105CSZ; Bacteria.
eggNOG; COG0854; LUCA.
HOGENOM; HOG000258095; -.
InParanoid; P0A794; -.
KO; K03474; -.
OMA; TSNAGWD; -.
PhylomeDB; P0A794; -.
BioCyc; EcoCyc:PDXJ-MONOMER; -.
BioCyc; MetaCyc:PDXJ-MONOMER; -.
BRENDA; 2.6.99.2; 2026.
UniPathway; UPA00244; UER00313.
EvolutionaryTrace; P0A794; -.
PRO; PR:P0A794; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
GO; GO:0033856; F:pyridoxine 5'-phosphate synthase activity; IDA:EcoCyc.
GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoliWiki.
CDD; cd00003; PNPsynthase; 1.
Gene3D; 3.20.20.70; -; 1.
HAMAP; MF_00279; PdxJ; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR004569; PyrdxlP_synth_PdxJ.
InterPro; IPR036130; Pyridoxine-5'_phos_synth.
PANTHER; PTHR30456; PTHR30456; 1.
Pfam; PF03740; PdxJ; 1.
SUPFAM; SSF63892; SSF63892; 1.
TIGRFAMs; TIGR00559; pdxJ; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
Pyridoxine biosynthesis; Reference proteome; Transferase.
INIT_MET 1 1 Removed.
CHAIN 2 243 Pyridoxine 5'-phosphate synthase.
/FTId=PRO_0000190114.
REGION 11 12 1-deoxy-D-xylulose 5-phosphate binding.
REGION 215 216 3-amino-2-oxopropyl phosphate binding.
ACT_SITE 45 45 Proton acceptor.
ACT_SITE 72 72 Proton acceptor.
ACT_SITE 193 193 Proton donor.
BINDING 9 9 3-amino-2-oxopropyl phosphate.
BINDING 20 20 3-amino-2-oxopropyl phosphate.
BINDING 47 47 1-deoxy-D-xylulose 5-phosphate.
BINDING 52 52 1-deoxy-D-xylulose 5-phosphate.
BINDING 102 102 1-deoxy-D-xylulose 5-phosphate.
BINDING 194 194 3-amino-2-oxopropyl phosphate; via amide
nitrogen.
SITE 153 153 Transition state stabilizer.
VARIANT 194 194 G -> S (in pdxH null mutation
suppressor).
{ECO:0000269|PubMed:8636054}.
STRAND 5 9 {ECO:0000244|PDB:1M5W}.
HELIX 11 18 {ECO:0000244|PDB:1M5W}.
STRAND 20 22 {ECO:0000244|PDB:1HO4}.
HELIX 27 35 {ECO:0000244|PDB:1M5W}.
TURN 36 38 {ECO:0000244|PDB:1M5W}.
STRAND 40 45 {ECO:0000244|PDB:1M5W}.
STRAND 51 53 {ECO:0000244|PDB:1M5W}.
HELIX 55 64 {ECO:0000244|PDB:1M5W}.
STRAND 66 73 {ECO:0000244|PDB:1M5W}.
HELIX 77 86 {ECO:0000244|PDB:1M5W}.
STRAND 89 93 {ECO:0000244|PDB:1M5W}.
TURN 98 100 {ECO:0000244|PDB:1HO1}.
STRAND 103 105 {ECO:0000244|PDB:1IXP}.
HELIX 110 112 {ECO:0000244|PDB:1M5W}.
HELIX 113 125 {ECO:0000244|PDB:1M5W}.
STRAND 129 134 {ECO:0000244|PDB:1M5W}.
HELIX 138 146 {ECO:0000244|PDB:1M5W}.
STRAND 150 155 {ECO:0000244|PDB:1M5W}.
HELIX 157 161 {ECO:0000244|PDB:1M5W}.
HELIX 165 184 {ECO:0000244|PDB:1M5W}.
STRAND 188 194 {ECO:0000244|PDB:1M5W}.
TURN 197 199 {ECO:0000244|PDB:1M5W}.
HELIX 200 204 {ECO:0000244|PDB:1M5W}.
STRAND 209 214 {ECO:0000244|PDB:1M5W}.
HELIX 216 225 {ECO:0000244|PDB:1M5W}.
HELIX 227 242 {ECO:0000244|PDB:1M5W}.
SEQUENCE 243 AA; 26384 MW; BF513A5B844E8CB2 CRC64;
MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI
LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE VTTEGGLDVA GQRDKMRDAC
KRLADAGIQV SLFIDADEEQ IKAAAEVGAP FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT
FAASLGLKVN AGHGLTYHNV KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE
ARG


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