ISPF_PLAF7
ID ISPF_PLAF7 Reviewed; 240 AA.
AC P62368; A0A143ZWM3; O96178;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, apicoplast {ECO:0000303|PubMed:24410837};
DE Short=MECDP-synthase {ECO:0000305};
DE Short=MECPS {ECO:0000305};
DE EC=4.6.1.12 {ECO:0000250|UniProtKB:P62369};
DE AltName: Full=PfIspF {ECO:0000303|PubMed:24410837};
DE Flags: Precursor;
GN Name=IspF {ECO:0000303|PubMed:24410837}; ORFNames=PF3D7_0209300, PFB0420w;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=3D7;
RX PubMed=9804551; DOI=10.1126/science.282.5391.1126;
RA Gardner M.J., Tettelin H., Carucci D.J., Cummings L.M., Aravind L.,
RA Koonin E.V., Shallom S.J., Mason T., Yu K., Fujii C., Pederson J., Shen K.,
RA Jing J., Aston C., Lai Z., Schwartz D.C., Pertea M., Salzberg S.L.,
RA Zhou L., Sutton G.G., Clayton R., White O., Smith H.O., Fraser C.M.,
RA Adams M.D., Venter J.C., Hoffman S.L.;
RT "Chromosome 2 sequence of the human malaria parasite Plasmodium
RT falciparum.";
RL Science 282:1126-1132(1998).
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 X-RAY CRYSTALLOGRAPHY (1.56 ANGSTROMS) OF 60-240 IN COMPLEX WITH ZINC IONS
RP AND CDP, SUBUNIT, AND COFACTOR.
RX PubMed=24410837; DOI=10.1186/1472-6807-14-1;
RA O'Rourke P.E., Kalinowska-Tluscik J., Fyfe P.K., Dawson A., Hunter W.N.;
RT "Crystal structures of IspF from Plasmodium falciparum and Burkholderia
RT cenocepacia: comparisons inform antimicrobial drug target assessment.";
RL BMC Struct. Biol. 14:1-1(2014).
CC -!- FUNCTION: In the mevalonate-independent isoprenoid biosynthetic
CC pathway, converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate
CC into 2C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP.
CC {ECO:0000250|UniProtKB:P62369}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-
CC erythritol 2,4-cyclic diphosphate + CMP; Xref=Rhea:RHEA:23864,
CC ChEBI:CHEBI:57919, ChEBI:CHEBI:58483, ChEBI:CHEBI:60377; EC=4.6.1.12;
CC Evidence={ECO:0000250|UniProtKB:P62369};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:24410837};
CC Note=Binds 1 divalent metal cation per subunit.
CC {ECO:0000269|PubMed:24410837};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 4/6. {ECO:0000250|UniProtKB:P62369}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000305|PubMed:24410837}.
CC -!- SUBCELLULAR LOCATION: Plastid, apicoplast {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000305}.
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DR EMBL; LN999943; CZT98107.1; -; Genomic_DNA.
DR PIR; B71615; B71615.
DR RefSeq; XP_001349603.1; XM_001349567.1.
DR PDB; 4C81; X-ray; 1.56 A; A=60-240.
DR PDB; 4C82; X-ray; 2.00 A; A=60-240.
DR PDBsum; 4C81; -.
DR PDBsum; 4C82; -.
DR AlphaFoldDB; P62368; -.
DR SMR; P62368; -.
DR BioGRID; 1208005; 1.
DR IntAct; P62368; 1.
DR STRING; 5833.PFB0420w; -.
DR EnsemblProtists; CZT98107; CZT98107; PF3D7_0209300.
DR GeneID; 812685; -.
DR KEGG; pfa:PF3D7_0209300; -.
DR VEuPathDB; PlasmoDB:PF3D7_0209300; -.
DR HOGENOM; CLU_084630_2_0_1; -.
DR InParanoid; P62368; -.
DR OMA; QHFGTGR; -.
DR PhylomeDB; P62368; -.
DR BRENDA; 4.6.1.12; 4889.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000001450; Chromosome 2.
DR GO; GO:0020011; C:apicoplast; IDA:GeneDB.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniPathway.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:InterPro.
DR CDD; cd00554; MECDP_synthase; 1.
DR Gene3D; 3.30.1330.50; -; 1.
DR HAMAP; MF_00107; IspF; 1.
DR InterPro; IPR003526; MECDP_synthase.
DR InterPro; IPR020555; MECDP_synthase_CS.
DR InterPro; IPR036571; MECDP_synthase_sf.
DR PANTHER; PTHR43181; PTHR43181; 1.
DR Pfam; PF02542; YgbB; 1.
DR SUPFAM; SSF69765; SSF69765; 1.
DR TIGRFAMs; TIGR00151; ispF; 1.
DR PROSITE; PS01350; ISPF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Apicoplast; Isoprene biosynthesis; Lyase; Metal-binding;
KW Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..?
FT /note="Apicoplast"
FT /evidence="ECO:0000305"
FT CHAIN ?..240
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase, apicoplast"
FT /id="PRO_0000016484"
FT BINDING 71..73
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 71
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24410837,
FT ECO:0007744|PDB:4C81, ECO:0007744|PDB:4C82"
FT BINDING 73
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24410837,
FT ECO:0007744|PDB:4C81, ECO:0007744|PDB:4C82"
FT BINDING 115..116
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 123
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24410837,
FT ECO:0007744|PDB:4C81, ECO:0007744|PDB:4C82"
FT BINDING 137..139
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000269|PubMed:24410837,
FT ECO:0007744|PDB:4C81"
FT BINDING 142..146
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 181..187
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000269|PubMed:24410837,
FT ECO:0007744|PDB:4C81"
FT BINDING 212..214
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000269|PubMed:24410837,
FT ECO:0007744|PDB:4C81"
FT SITE 115
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT SITE 214
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT STRAND 65..77
FT /evidence="ECO:0007829|PDB:4C81"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:4C81"
FT STRAND 105..116
FT /evidence="ECO:0007829|PDB:4C81"
FT HELIX 120..133
FT /evidence="ECO:0007829|PDB:4C81"
FT HELIX 138..141
FT /evidence="ECO:0007829|PDB:4C81"
FT HELIX 153..167
FT /evidence="ECO:0007829|PDB:4C81"
FT STRAND 170..180
FT /evidence="ECO:0007829|PDB:4C81"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:4C81"
FT HELIX 186..201
FT /evidence="ECO:0007829|PDB:4C81"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:4C81"
FT STRAND 208..213
FT /evidence="ECO:0007829|PDB:4C81"
FT HELIX 219..222
FT /evidence="ECO:0007829|PDB:4C81"
FT STRAND 225..237
FT /evidence="ECO:0007829|PDB:4C81"
SQ SEQUENCE 240 AA; 27161 MW; 7C46116F48B33D15 CRC64;
MFLKGYTSNV VLIILTFFIL LTKEEKNIKN NISGYCFLNF GLKKNAIIKK REKQNLKLFC
YNGIRIGQGY DIHKIKVLDE EYNTYANNDF NKNEQSFKTL TLGGVKINNV LVLSHSDGDI
IYHSIVDSIL GALGSLDIGT LFPDKDEKNK NKNSAIFLRY ARLLIYKKNY DIGNVDINVI
AQVPKISNIR KNIIKNISTV LNIDESQISV KGKTHEKLGV IGEKKAIECF ANILLIPKNS
