ISPF_BURCJ
ID ISPF_BURCJ Reviewed; 161 AA.
AC B4EC22;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000255|HAMAP-Rule:MF_00107};
DE Short=MECDP-synthase {ECO:0000255|HAMAP-Rule:MF_00107};
DE Short=MECPP-synthase {ECO:0000255|HAMAP-Rule:MF_00107};
DE Short=MECPS {ECO:0000255|HAMAP-Rule:MF_00107};
DE EC=4.6.1.12 {ECO:0000255|HAMAP-Rule:MF_00107};
GN Name=ispF {ECO:0000255|HAMAP-Rule:MF_00107};
GN OrderedLocusNames=BceJ2315_19780; ORFNames=BCAL2015;
OS Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 /
OS NCTC 13227 / J2315 / CF5610) (Burkholderia cepacia (strain J2315)).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX NCBI_TaxID=216591;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610;
RX PubMed=18931103; DOI=10.1128/jb.01230-08;
RA Holden M.T., Seth-Smith H.M., Crossman L.C., Sebaihia M., Bentley S.D.,
RA Cerdeno-Tarraga A.M., Thomson N.R., Bason N., Quail M.A., Sharp S.,
RA Cherevach I., Churcher C., Goodhead I., Hauser H., Holroyd N., Mungall K.,
RA Scott P., Walker D., White B., Rose H., Iversen P., Mil-Homens D.,
RA Rocha E.P., Fialho A.M., Baldwin A., Dowson C., Barrell B.G., Govan J.R.,
RA Vandamme P., Hart C.A., Mahenthiralingam E., Parkhill J.;
RT "The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of
RT cystic fibrosis patients.";
RL J. Bacteriol. 191:261-277(2009).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH ZINC IONS AND CMP,
RP 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: Involved in the biosynthesis of isopentenyl diphosphate (IPP)
CC and dimethylallyl diphosphate (DMAPP), two major building blocks of
CC isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-
CC C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol
CC 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine
CC 5-monophosphate (CMP). {ECO:0000255|HAMAP-Rule:MF_00107}.
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:0000255|HAMAP-Rule:MF_00107};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00107,
CC ECO:0000269|PubMed:24410837};
CC Note=Binds 1 divalent metal cation per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00107, 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:0000255|HAMAP-Rule:MF_00107}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00107,
CC ECO:0000305|PubMed:24410837}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000255|HAMAP-
CC Rule:MF_00107}.
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DR EMBL; AM747720; CAR52315.1; -; Genomic_DNA.
DR RefSeq; WP_006488015.1; NC_011000.1.
DR PDB; 4C8E; X-ray; 1.90 A; A/B/C=1-161.
DR PDB; 4C8G; X-ray; 2.00 A; A/B/C=1-161.
DR PDB; 4C8I; X-ray; 2.00 A; A/B/C=1-161.
DR PDBsum; 4C8E; -.
DR PDBsum; 4C8G; -.
DR PDBsum; 4C8I; -.
DR AlphaFoldDB; B4EC22; -.
DR SMR; B4EC22; -.
DR STRING; 216591.BCAL2015; -.
DR EnsemblBacteria; CAR52315; CAR52315; BCAL2015.
DR GeneID; 56558498; -.
DR KEGG; bcj:BCAL2015; -.
DR eggNOG; COG0245; Bacteria.
DR HOGENOM; CLU_084630_2_0_4; -.
DR OMA; QHFGTGR; -.
DR OrthoDB; 1716560at2; -.
DR BioCyc; BCEN216591:G1G1V-2213-MON; -.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000001035; Chromosome 1.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IEA:UniProtKB-UniRule.
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:UniProtKB-UniRule.
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; Isoprene biosynthesis; Lyase; Metal-binding.
FT CHAIN 1..161
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /id="PRO_1000094243"
FT BINDING 10..12
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 10
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 12
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 36..37
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 40..48
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 44
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 58..60
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 63..67
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 102..108
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 133..137
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 144
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT SITE 36
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT SITE 135
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT STRAND 2..15
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 20..22
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:4C8G"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:4C8G"
FT HELIX 41..53
FT /evidence="ECO:0007829|PDB:4C8E"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:4C8I"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:4C8E"
FT HELIX 75..88
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 91..101
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:4C8E"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:4C8E"
FT HELIX 111..122
FT /evidence="ECO:0007829|PDB:4C8E"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:4C8E"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:4C8E"
FT STRAND 146..158
FT /evidence="ECO:0007829|PDB:4C8E"
SQ SEQUENCE 161 AA; 16923 MW; B11727467A3E9C50 CRC64;
MDFRIGQGYD VHQLVEGRPL IIGGVTIPYE RGLLGHSDAD VLLHAITDAL FGAAALGDIG
RHFSDTDAAF KGADSRVLLR ACAERVKAAG FTIQNVDSTV IAQAPKLAPH IDGMRANIAA
DLGLPLERVN VKAKTNEKLG YLGRGEGIEA QAAALLVKQG G
