ID T5DFG6_HELPX Unreviewed; 618 AA.
AC T5DFG6;
DT 13-NOV-2013, integrated into UniProtKB/TrEMBL.
DT 13-NOV-2013, sequence version 1.
DT 27-MAR-2024, entry version 64.
DE RecName: Full=1-deoxy-D-xylulose-5-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_00315};
DE EC=2.2.1.7 {ECO:0000256|HAMAP-Rule:MF_00315};
DE AltName: Full=1-deoxyxylulose-5-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_00315};
DE Short=DXP synthase {ECO:0000256|HAMAP-Rule:MF_00315};
DE Short=DXPS {ECO:0000256|HAMAP-Rule:MF_00315};
GN Name=dxs {ECO:0000256|HAMAP-Rule:MF_00315};
GN ORFNames=N409_02190 {ECO:0000313|EMBL:EQL73668.1};
OS Helicobacter pylori FD719.
OC Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=1191286 {ECO:0000313|EMBL:EQL73668.1, ECO:0000313|Proteomes:UP000015963};
RN [1] {ECO:0000313|EMBL:EQL73668.1, ECO:0000313|Proteomes:UP000015963}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FD719 {ECO:0000313|EMBL:EQL73668.1,
RC ECO:0000313|Proteomes:UP000015963};
RX PubMed=23012278; DOI=10.1128/JB.01278-12;
RA Gunaletchumy S.P., Teh X., Khosravi Y., Ramli N.S., Chua E.G., Kavitha T.,
RA Mason J.N., Lee H.T., Alias H., Zaidan N.Z., Yassin N.B., Tay L.C.,
RA Rudd S., Mitchell H.M., Kaakoush N.O., Loke M.F., Goh K.L., Vadivelu J.;
RT "Draft genome sequences of Helicobacter pylori isolates from Malaysia,
RT cultured from patients with functional dyspepsia and gastric cancer.";
RL J. Bacteriol. 194:5695-5696(2012).
RN [2] {ECO:0000313|EMBL:EQL73668.1, ECO:0000313|Proteomes:UP000015963}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FD719 {ECO:0000313|EMBL:EQL73668.1,
RC ECO:0000313|Proteomes:UP000015963};
RX PubMed=24051312;
RA Rehvathy V., Tan M.H., Gunaletchumy S.P., Teh X., Wang S., Baybayan P.,
RA Singh S., Ashby M., Kaakoush N.O., Mitchell H.M., Croft L.J., Goh K.L.,
RA Loke M.F., Vadivelu J.;
RT "Multiple genome sequences of Helicobacter pylori strains of diverse
RT disease and antibiotic resistance backgrounds from malaysia.";
RL Genome Announc. 1:E00687-E00713(2013).
CC -!- FUNCTION: Catalyzes the acyloin condensation reaction between C atoms 2
CC and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-
CC xylulose-5-phosphate (DXP). {ECO:0000256|HAMAP-Rule:MF_00315}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-
CC xylulose 5-phosphate + CO2; Xref=Rhea:RHEA:12605, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57792,
CC ChEBI:CHEBI:59776; EC=2.2.1.7; Evidence={ECO:0000256|HAMAP-
CC Rule:MF_00315};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00315};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00315};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00315};
CC Note=Binds 1 thiamine pyrophosphate per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_00315};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-
CC phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-
CC glyceraldehyde 3-phosphate and pyruvate: step 1/1.
CC {ECO:0000256|ARBA:ARBA00004980, ECO:0000256|HAMAP-Rule:MF_00315}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|ARBA:ARBA00011738, ECO:0000256|HAMAP-
CC Rule:MF_00315}.
CC -!- SIMILARITY: Belongs to the transketolase family. DXPS subfamily.
CC {ECO:0000256|ARBA:ARBA00011081, ECO:0000256|HAMAP-Rule:MF_00315}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EQL73668.1}.
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DR EMBL; AKHU02000013; EQL73668.1; -; Genomic_DNA.
DR AlphaFoldDB; T5DFG6; -.
DR PATRIC; fig|1191286.4.peg.1355; -.
DR UniPathway; UPA00064; UER00091.
DR Proteomes; UP000015963; Unassembled WGS sequence.
DR GO; GO:0008661; F:1-deoxy-D-xylulose-5-phosphate synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0052865; P:1-deoxy-D-xylulose 5-phosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009228; P:thiamine biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd02007; TPP_DXS; 1.
DR CDD; cd07033; TPP_PYR_DXS_TK_like; 1.
DR Gene3D; 3.40.50.920; -; 1.
DR Gene3D; 3.40.50.970; -; 2.
DR HAMAP; MF_00315; DXP_synth; 1.
DR InterPro; IPR005477; Dxylulose-5-P_synthase.
DR InterPro; IPR004045; Glutathione_S-Trfase_N.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR009014; Transketo_C/PFOR_II.
DR InterPro; IPR005475; Transketolase-like_Pyr-bd.
DR InterPro; IPR020826; Transketolase_BS.
DR InterPro; IPR033248; Transketolase_C.
DR InterPro; IPR049557; Transketolase_CS.
DR NCBIfam; TIGR00204; dxs; 1.
DR PANTHER; PTHR43322; 1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED; 1.
DR PANTHER; PTHR43322:SF5; 1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE, CHLOROPLASTIC; 1.
DR Pfam; PF13292; DXP_synthase_N; 1.
DR Pfam; PF02779; Transket_pyr; 1.
DR Pfam; PF02780; Transketolase_C; 1.
DR SMART; SM00861; Transket_pyr; 1.
DR SUPFAM; SSF52518; Thiamin diphosphate-binding fold (THDP-binding); 2.
DR SUPFAM; SSF52922; TK C-terminal domain-like; 1.
DR PROSITE; PS50404; GST_NTER; 1.
DR PROSITE; PS00801; TRANSKETOLASE_1; 1.
DR PROSITE; PS00802; TRANSKETOLASE_2; 1.
PE 3: Inferred from homology;
KW Isoprene biosynthesis {ECO:0000256|ARBA:ARBA00023229, ECO:0000256|HAMAP-
KW Rule:MF_00315};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00315};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00315};
KW Thiamine biosynthesis {ECO:0000256|ARBA:ARBA00022977, ECO:0000256|HAMAP-
KW Rule:MF_00315};
KW Thiamine pyrophosphate {ECO:0000256|ARBA:ARBA00023052, ECO:0000256|HAMAP-
KW Rule:MF_00315};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00315}.
FT DOMAIN 496..576
FT /note="GST N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS50404"
FT BINDING 70
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 111..113
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 142
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 143..144
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 171
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 171
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 278
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
FT BINDING 360
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00315"
SQ SEQUENCE 618 AA; 67710 MW; B989AC6333A41EE8 CRC64;
MILQNKTFDL NPNDIASLEL VCQTLRSRIL EVVSANGGHL SSSLGAVELI VGMHALFDCQ
KNPFIFDTSH QAYAHKLLTG RFESFSTLRQ FKGLSGFTKP SESVYDYFIA GHSSTSVSIG
VGVAKAFCLK QALGMPIALL GDGSISAGIF YEALNELGDR KYPMIMILND NEMSISTPIG
ALSKALSQLM KGPFYQSFRS KVKKILSTLP ESVNYLASRF EESFKLITPG VFFEELGINY
IGPINGHDLS AIIETLKLAK ELKEPVLIHA QTLKGKGYKI AEGRYEKWHG VGPFDLDTGL
SKKSKSAILS PTEAYSNTLL ELAKKDEKIV GVTAAMPSGT GLDKLIDAYP LRFFDVAIAE
QHALTSSSAM AKEGFKPFVS IYSTFLQRAY DSIVHDACIS SLPIKLAIDR AGIVGEDGET
HQGLLDVSYL RSIPNMVIFA PRDNETLKNA VRFANEHDSS PCAFRYPRGS FALKEGVFEP
SGFVLGQSEL LKKEGEILLI GYGNGVGRAH LVQLALKEKN IECALLDLRF LKPLDQNLSA
IIAPYQKLYV FSDNYKLGGV ASAILEFLSE QNILKPVKSF EIIDEFIMHG NTALVEKSLG
LDTESLTDAI LKDLGQER
//
