ISPDF_BRADU
ID ISPDF_BRADU Reviewed; 398 AA.
AC Q89LQ8;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 109.
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=bll4485;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
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; BA000040; BAC49750.1; -; Genomic_DNA.
DR RefSeq; NP_771125.1; NC_004463.1.
DR RefSeq; WP_011087257.1; NZ_CP011360.1.
DR AlphaFoldDB; Q89LQ8; -.
DR SMR; Q89LQ8; -.
DR STRING; 224911.27352748; -.
DR EnsemblBacteria; BAC49750; BAC49750; BAC49750.
DR GeneID; 64024231; -.
DR KEGG; bja:bll4485; -.
DR PATRIC; fig|224911.44.peg.4260; -.
DR eggNOG; COG0245; Bacteria.
DR eggNOG; COG1211; Bacteria.
DR HOGENOM; CLU_042800_2_3_5; -.
DR InParanoid; Q89LQ8; -.
DR OMA; TGYDVHA; -.
DR PhylomeDB; Q89LQ8; -.
DR UniPathway; UPA00056; UER00093.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IBA:GO_Central.
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; Reference proteome; Transferase.
FT CHAIN 1..398
FT /note="Bifunctional enzyme IspD/IspF"
FT /id="PRO_0000075658"
FT REGION 1..234
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT REGION 235..398
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 241..243
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 241
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 243
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 267..268
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 275
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT BINDING 289..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 365..368
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 372
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 375
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 19
FT /note="Transition state stabilizer"
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 156
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 213
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 267
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT SITE 366
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
SQ SEQUENCE 398 AA; 42226 MW; 93E0A201CB315B6A CRC64;
MAKSQRTAVV LVAAGRGLRA GAGGPKQYRE IGGQPVIYRA MEAFSRHPDV FAVQPVVNPD
DSAMFTAAVA GLKHEPPTNG GATRQASVLA GLEALAKHQP DIVLIHDAAR PFVSDGVISR
AIDAASRTGA AIPVVPVTDT IKLTGASGNV EDTPDRARLR IAQTPQSFRF DVILEAHRRA
AKDGRSDFTD DAAIAEWAGL TVATFEGDVA NMKLTTPEDF VREEARLAAQ LGDIRTGTGY
DVHAFGEGDH VMICGVRVPH SKGFLAHSDG DVGLHALVDA ILGALADGDI GSHFPPSDAK
WKGASSDQFL KYAIERVAQR GGRVANLEVT MICERPKIGP LRDTMRARIA EISGVDISRV
AVKATTSERL GFTGREEGIA ATASATIRLP FNEKTWSV
