ISPDF_RHILO
ID ISPDF_RHILO Reviewed; 407 AA.
AC Q98MX9;
DT 06-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 115.
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=mll0395;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
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; BA000012; BAB47984.1; -; Genomic_DNA.
DR RefSeq; WP_010909341.1; NC_002678.2.
DR AlphaFoldDB; Q98MX9; -.
DR SMR; Q98MX9; -.
DR STRING; 266835.14021371; -.
DR EnsemblBacteria; BAB47984; BAB47984; BAB47984.
DR GeneID; 66684136; -.
DR KEGG; mlo:mll0395; -.
DR eggNOG; COG0245; Bacteria.
DR eggNOG; COG1211; Bacteria.
DR HOGENOM; CLU_042800_1_0_5; -.
DR OMA; TGYDVHA; -.
DR OrthoDB; 525632at2; -.
DR UniPathway; UPA00056; UER00093.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000000552; 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 PANTHER; PTHR43181; PTHR43181; 1.
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..407
FT /note="Bifunctional enzyme IspD/IspF"
FT /id="PRO_0000075673"
FT REGION 1..246
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT REGION 247..407
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 253..255
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 253
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 255
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 279..280
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 287
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 301..303
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 377..380
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 384
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 387
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 26
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 34
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 165
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 222
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 279
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 378
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
SQ SEQUENCE 407 AA; 42834 MW; FCEE6A5B4CD34F33 CRC64;
MTEASENASA TGGVAVVIVA AGRGARAGQA NGPKQYQNIG GRAVIAHTLE IFLAHPRTDR
IVVAIHADDH ELFRQAAGSQ AERVTAIIGG PTRQESVRLG LLALKEHAPG QVLIHDAVRP
FVDADLIDRT ISAIGENEGA LPALPVADTL KRESAAGVVA ETVSRSGLHA AQTPQGFPYG
PILAAHDKAF QLGRLDFTDD AAIAEWAHIP VKLVPGSPDN VKLTWARDIA MAHQRLSSER
THFPDIRTGN GYDVHAFEPG DHVTLCGVAI PHDKKLSGHS DADVGLHALT DALLATCGAG
DIGTHFPPSD PQWKGAASRI FVEHAAKVVR QRGGRIANAD ITLICEAPRV GPHREAMTAA
LSRMLGISAD RISIKATTNE KLGFVGREEG IAAIATASVV FPGEVPE
