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ISPDF_SOLM1
ID   ISPDF_SOLM1             Reviewed;         400 AA.
AC   C4XSW4;
DT   22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT   28-JUL-2009, sequence version 1.
DT   03-AUG-2022, entry version 73.
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=DMR_23150;
OS   Solidesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)
OS   (Desulfovibrio magneticus).
OC   Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC   Desulfovibrionaceae; Solidesulfovibrio.
OX   NCBI_TaxID=573370;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700980 / DSM 13731 / RS-1;
RX   PubMed=19675025; DOI=10.1101/gr.088906.108;
RA   Nakazawa H., Arakaki A., Narita-Yamada S., Yashiro I., Jinno K., Aoki N.,
RA   Tsuruyama A., Okamura Y., Tanikawa S., Fujita N., Takeyama H.,
RA   Matsunaga T.;
RT   "Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed
RT   common gene clusters in magnetotactic bacteria.";
RL   Genome Res. 19:1801-1808(2009).
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; AP010904; BAH75806.1; -; Genomic_DNA.
DR   RefSeq; WP_015860988.1; NC_012796.1.
DR   AlphaFoldDB; C4XSW4; -.
DR   SMR; C4XSW4; -.
DR   STRING; 573370.DMR_23150; -.
DR   EnsemblBacteria; BAH75806; BAH75806; DMR_23150.
DR   KEGG; dma:DMR_23150; -.
DR   eggNOG; COG0245; Bacteria.
DR   eggNOG; COG1211; Bacteria.
DR   HOGENOM; CLU_042800_2_4_7; -.
DR   OMA; TGYDVHA; -.
DR   UniPathway; UPA00056; UER00093.
DR   UniPathway; UPA00056; UER00095.
DR   Proteomes; UP000009071; 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; -; 1.
DR   Gene3D; 3.90.550.10; -; 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   Pfam; PF01128; IspD; 1.
DR   Pfam; PF02542; YgbB; 1.
DR   SUPFAM; SSF53448; SSF53448; 1.
DR   SUPFAM; SSF69765; SSF69765; 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; Lyase; Metal-binding; Multifunctional enzyme;
KW   Nucleotidyltransferase; Transferase.
FT   CHAIN           1..400
FT                   /note="Bifunctional enzyme IspD/IspF"
FT                   /id="PRO_1000215367"
FT   REGION          1..235
FT                   /note="2-C-methyl-D-erythritol 4-phosphate
FT                   cytidylyltransferase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   REGION          236..400
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         242..244
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         242
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         244
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         276..277
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         284
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         298..300
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         303..307
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         374..377
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         381
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            15
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            25
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            161
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            216
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            276
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            375
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
SQ   SEQUENCE   400 AA;  42047 MW;  F7DFF9AEE7CF390C CRC64;
     MSLWTVLLAA GSGTRLAQAS GGVKKQFLSV GGRPLYWKAL TAFAKSPDVA GVVVVFAPED
     LAEATRELAG FLDANHPGLP VLTAAGGARR QDSVKNGLDA LPREARLVLI HDAARPFVDA
     GLIARVADAL AAGRKAVIPT LPVTDTVKQV DGDRVTATLP RHELAAVQTP QGFDLTLLRQ
     AYAHARPDFD VTDDASLVEH YGQPVFTVPG APRNMKITHP EDLASLAEAA APPVPVTGYG
     YDVHRYADPR NPGKQPPRPM KLGGFPILGA PEVLAHSDGD VLLHALTDAV LGCVAGGDIG
     RLFPDSNPDF DNMASGVFLS EALLAAKAKG LTITHVDLTI IAQIPKISPH AEAIRLNVAA
     LLGLNKEQVN LKATTEEGLG FTGEKKGIKA VALVSGWRRP
 
 
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