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Database: UniProt
Entry: ISPDF_CLAM3
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Original site: ISPDF_CLAM3 
ID   ISPDF_CLAM3             Reviewed;         410 AA.
AC   A5CTY4;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   12-JUN-2007, sequence version 1.
DT   24-JAN-2024, entry version 96.
DE   RecName: Full=Bifunctional enzyme IspD/IspF {ECO:0000255|HAMAP-Rule:MF_01520};
DE   Includes:
DE     RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              EC=2.7.7.60 {ECO:0000255|HAMAP-Rule:MF_01520};
DE     AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE     AltName: Full=MEP cytidylyltransferase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MCT {ECO:0000255|HAMAP-Rule:MF_01520};
DE   Includes:
DE     RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MECDP-synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MECPP-synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MECPS {ECO:0000255|HAMAP-Rule:MF_01520};
DE              EC=4.6.1.12 {ECO:0000255|HAMAP-Rule:MF_01520};
GN   Name=ispDF {ECO:0000255|HAMAP-Rule:MF_01520}; OrderedLocusNames=CMM_2489;
OS   Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382).
OC   Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae;
OC   Clavibacter.
OX   NCBI_TaxID=443906;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=NCPPB 382;
RX   PubMed=18192381; DOI=10.1128/jb.01595-07;
RA   Gartemann K.-H., Abt B., Bekel T., Burger A., Engemann J., Fluegel M.,
RA   Gaigalat L., Goesmann A., Graefen I., Kalinowski J., Kaup O., Kirchner O.,
RA   Krause L., Linke B., McHardy A., Meyer F., Pohle S., Rueckert C.,
RA   Schneiker S., Zellermann E.-M., Puehler A., Eichenlaub R., Kaiser O.,
RA   Bartels D.;
RT   "The genome sequence of the tomato-pathogenic actinomycete Clavibacter
RT   michiganensis subsp. michiganensis NCPPB382 reveals a large island involved
RT   in pathogenicity.";
RL   J. Bacteriol. 190:2138-2149(2008).
CC   -!- FUNCTION: Bifunctional enzyme that catalyzes the formation of 4-
CC       diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-
CC       erythritol 4-phosphate (MEP) (IspD), and catalyzes the conversion of 4-
CC       diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-
CC       methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding
CC       release of cytidine 5-monophosphate (CMP) (IspF). {ECO:0000255|HAMAP-
CC       Rule:MF_01520}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-
CC         methyl-D-erythritol + diphosphate; Xref=Rhea:RHEA:13429,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, ChEBI:CHEBI:37563,
CC         ChEBI:CHEBI:57823, ChEBI:CHEBI:58262; EC=2.7.7.60;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01520};
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_01520};
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01520};
CC   -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC       via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC       phosphate: step 2/6. {ECO:0000255|HAMAP-Rule:MF_01520}.
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_01520}.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the IspD/TarI
CC       cytidylyltransferase family. IspD subfamily. {ECO:0000255|HAMAP-
CC       Rule:MF_01520}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the IspF family.
CC       {ECO:0000255|HAMAP-Rule:MF_01520}.
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DR   EMBL; AM711867; CAN02570.1; -; Genomic_DNA.
DR   RefSeq; WP_012039177.1; NC_009480.1.
DR   AlphaFoldDB; A5CTY4; -.
DR   SMR; A5CTY4; -.
DR   KEGG; cmi:CMM_2489; -.
DR   eggNOG; COG0245; Bacteria.
DR   eggNOG; COG1211; Bacteria.
DR   HOGENOM; CLU_042800_2_5_11; -.
DR   OMA; TGYDVHA; -.
DR   OrthoDB; 9802561at2; -.
DR   UniPathway; UPA00056; UER00093.
DR   UniPathway; UPA00056; UER00095.
DR   Proteomes; UP000001564; Chromosome.
DR   GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0050518; F:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 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; cd02516; CDP-ME_synthetase; 1.
DR   CDD; cd00554; MECDP_synthase; 1.
DR   Gene3D; 3.30.1330.50; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; 1.
DR   HAMAP; MF_00108; IspD; 1.
DR   HAMAP; MF_01520; IspDF; 1.
DR   HAMAP; MF_00107; IspF; 1.
DR   InterPro; IPR001228; IspD.
DR   InterPro; IPR026596; IspD/F.
DR   InterPro; IPR034683; IspD/TarI.
DR   InterPro; IPR018294; ISPD_synthase_CS.
DR   InterPro; IPR003526; MECDP_synthase.
DR   InterPro; IPR020555; MECDP_synthase_CS.
DR   InterPro; IPR036571; MECDP_synthase_sf.
DR   InterPro; IPR029044; Nucleotide-diphossugar_trans.
DR   NCBIfam; TIGR00453; ispD; 1.
DR   NCBIfam; TIGR00151; ispF; 1.
DR   PANTHER; PTHR43181; 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC; 1.
DR   PANTHER; PTHR43181:SF1; 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC; 1.
DR   Pfam; PF01128; IspD; 1.
DR   Pfam; PF02542; YgbB; 1.
DR   SUPFAM; SSF69765; IpsF-like; 1.
DR   SUPFAM; SSF53448; Nucleotide-diphospho-sugar transferases; 1.
DR   PROSITE; PS01295; ISPD; 1.
DR   PROSITE; PS01350; ISPF; 1.
PE   3: Inferred from homology;
KW   Isoprene biosynthesis; Lyase; Metal-binding; Multifunctional enzyme;
KW   Nucleotidyltransferase; Transferase.
FT   CHAIN           1..410
FT                   /note="Bifunctional enzyme IspD/IspF"
FT                   /id="PRO_0000315552"
FT   REGION          1..257
FT                   /note="2-C-methyl-D-erythritol 4-phosphate
FT                   cytidylyltransferase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   REGION          258..410
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         264..266
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         264
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         266
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         290..291
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         298
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         312..314
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         385..388
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         392
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         395
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            35
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            42
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            177
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            230
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            290
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            386
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
SQ   SEQUENCE   410 AA;  40906 MW;  987E4DA39C126EF3 CRC64;
     MSHDPVVPSA PATDGGATDG PRLGVVVVAA GSGTRLGAGI PKALVEVGGV TLLARSLSSV
     LGLAEEAHVV VVAPDTHLAE TSAVVDAVAG AARGSVAVVV GGATRQGSVR AGLAALVGSV
     DTVLVHDAAR ALTPTDLFAA VARAVRAEGA GVVPGLPVTD TVKRVDPAGE CLGTVDRSDL
     VGVQTPQGFP RAALDAAYAR AAAEHTDDAA LFQASGGRVR VIPGDALAFK VTTAWDLRRA
     EELVARDAGA GSASSRLRSG IGTDVHAVDA SQPLWLAGLH WPGEAGLAGH SDGDAVSHAM
     CDALLSAAGL GDIGGIFGTD DPELDGAHGE VFLRRTAELV RDAGYRIVNV AVQVMAVRPK
     LSPRRAEAER ILSAAVGAPV SLAGTTTDGL GFTGRGDGVA AVATALVERL
//
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