ID A0A0D6Q9J5_KOMXY Unreviewed; 396 AA. AC A0A0D6Q9J5; DT 27-MAY-2015, integrated into UniProtKB/TrEMBL. DT 27-MAY-2015, sequence version 1. DT 22-FEB-2023, entry version 49. DE RecName: Full=Bifunctional enzyme IspD/IspF {ECO:0000256|HAMAP-Rule:MF_01520}; DE Includes: DE RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase {ECO:0000256|HAMAP-Rule:MF_01520}; DE EC=2.7.7.60 {ECO:0000256|HAMAP-Rule:MF_01520}; DE AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase {ECO:0000256|HAMAP-Rule:MF_01520}; DE AltName: Full=MEP cytidylyltransferase {ECO:0000256|HAMAP-Rule:MF_01520}; DE Short=MCT {ECO:0000256|HAMAP-Rule:MF_01520}; DE Includes: DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000256|HAMAP-Rule:MF_01520}; DE Short=MECDP-synthase {ECO:0000256|HAMAP-Rule:MF_01520}; DE Short=MECPP-synthase {ECO:0000256|HAMAP-Rule:MF_01520}; DE Short=MECPS {ECO:0000256|HAMAP-Rule:MF_01520}; DE EC=4.6.1.12 {ECO:0000256|HAMAP-Rule:MF_01520}; GN Name=ispDF {ECO:0000256|HAMAP-Rule:MF_01520}; GN ORFNames=Gxy13693_024_061 {ECO:0000313|EMBL:GAN99645.1}; OS Komagataeibacter xylinus NBRC 13693. OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; OC Acetobacteraceae; Komagataeibacter. OX NCBI_TaxID=1234668 {ECO:0000313|EMBL:GAN99645.1, ECO:0000313|Proteomes:UP000032683}; RN [1] {ECO:0000313|EMBL:GAN99645.1, ECO:0000313|Proteomes:UP000032683} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=NBRC 13693 {ECO:0000313|EMBL:GAN99645.1, RC ECO:0000313|Proteomes:UP000032683}; RA Azuma Y., Higashiura N., Hirakawa H., Matsushita K.; RT "Whole genome sequence of Gluconacetobacter xylinus NBRC 13693."; RL Submitted (NOV-2012) to the EMBL/GenBank/DDBJ databases. 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:0000256|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:0000256|ARBA:ARBA00001282, ECO:0000256|HAMAP- CC 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:0000256|ARBA:ARBA00000200, ECO:0000256|HAMAP- CC Rule:MF_01520}; CC -!- COFACTOR: CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240; CC Evidence={ECO:0000256|ARBA:ARBA00001968, CC ECO:0000256|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:0000256|ARBA:ARBA00004787, ECO:0000256|HAMAP- CC 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:0000256|ARBA:ARBA00004709, ECO:0000256|HAMAP- CC Rule:MF_01520}. CC -!- SIMILARITY: Belongs to the IspD/TarI cytidylyltransferase family. IspD CC subfamily. {ECO:0000256|ARBA:ARBA00009789}. CC -!- SIMILARITY: Belongs to the IspF family. CC {ECO:0000256|ARBA:ARBA00008480}. CC -!- SIMILARITY: In the C-terminal section; belongs to the IspF family. CC {ECO:0000256|HAMAP-Rule:MF_01520}. CC -!- SIMILARITY: In the N-terminal section; belongs to the IspD/TarI CC cytidylyltransferase family. IspD subfamily. {ECO:0000256|HAMAP- CC Rule:MF_01520}. CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01520}. 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:GAN99645.1}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; BANJ01000024; GAN99645.1; -; Genomic_DNA. DR AlphaFoldDB; A0A0D6Q9J5; -. DR EnsemblBacteria; GAN99645; GAN99645; Gxy13693_024_061. DR UniPathway; UPA00056; UER00093. DR Proteomes; UP000032683; Unassembled WGS sequence. 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 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 TIGRFAMs; TIGR00453; ispD; 1. DR TIGRFAMs; TIGR00151; ispF; 1. DR PROSITE; PS01295; ISPD; 1. DR PROSITE; PS01350; ISPF; 1. PE 3: Inferred from homology; KW Isoprene biosynthesis {ECO:0000256|ARBA:ARBA00023229, ECO:0000256|HAMAP- KW Rule:MF_01520}; KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_01520}; KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP- KW Rule:MF_01520}; KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268, ECO:0000256|HAMAP- KW Rule:MF_01520}; KW Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_01520, KW ECO:0000313|EMBL:GAN99645.1}; Signal {ECO:0000256|SAM:SignalP}; KW Transferase {ECO:0000256|HAMAP-Rule:MF_01520, ECO:0000313|EMBL:GAN99645.1}. FT SIGNAL 1..16 FT /evidence="ECO:0000256|SAM:SignalP" FT CHAIN 17..396 FT /note="Bifunctional enzyme IspD/IspF" FT /evidence="ECO:0000256|SAM:SignalP" FT /id="PRO_5002310832" FT DOMAIN 241..393 FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate FT synthase" FT /evidence="ECO:0000259|Pfam:PF02542" FT REGION 1..240 FT /note="2-C-methyl-D-erythritol 4-phosphate FT cytidylyltransferase" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT REGION 241..396 FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate FT synthase" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 247..249 FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" FT /ligand_id="ChEBI:CHEBI:57919" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 247 FT /ligand="a divalent metal cation" FT /ligand_id="ChEBI:CHEBI:60240" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 249 FT /ligand="a divalent metal cation" FT /ligand_id="ChEBI:CHEBI:60240" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 273..274 FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" FT /ligand_id="ChEBI:CHEBI:57919" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 281 FT /ligand="a divalent metal cation" FT /ligand_id="ChEBI:CHEBI:60240" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 295..297 FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" FT /ligand_id="ChEBI:CHEBI:57919" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 371..374 FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" FT /ligand_id="ChEBI:CHEBI:57919" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 378 FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" FT /ligand_id="ChEBI:CHEBI:57919" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT BINDING 381 FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate" FT /ligand_id="ChEBI:CHEBI:57919" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT SITE 22 FT /note="Transition state stabilizer" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT SITE 33 FT /note="Transition state stabilizer" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT SITE 166 FT /note="Positions MEP for the nucleophilic attack" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT SITE 220 FT /note="Positions MEP for the nucleophilic attack" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT SITE 273 FT /note="Transition state stabilizer" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" FT SITE 372 FT /note="Transition state stabilizer" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520" SQ SEQUENCE 396 AA; 41962 MW; 32DA45C49511BAA2 CRC64; MAALLRIMRV AAILLAAGQG SRYSAQTATP LAKQYVTLGG RPVIRHAADA LAPHVGMIQP VGDPALLTGA LEGFAPAGCT VLPVVPGGAT RQASVSAGLE ALDRLPEDRR PDLVLIHDGA RPYVPADVTQ GVIAALEQHA GVIPAVPVAD TIKRAKDGII TDTVPRTDLF RAQTPQGFRF ALLRDLHRAA DAADATDDAA LLEQAGHHVA IVPGSEDNIK LTYKEDLVRL ERLIGPTLLP RTGMGYDVHA FAENRPLIMC GINVPHTRGL AGHSDADVGI HALCDAIYGA LAEGDIGRHF PPSQNEWKDA DSARFLVHAG ERIRLRGGML VNADVTLICE RPKIGPHSEA MRARLADLLK VDVDRISVKA TTSERLGFTG REEGIACLAS ATVLVP //