ID A0A1I2QXU8_9SPHN Unreviewed; 394 AA.
AC A0A1I2QXU8;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 24-JAN-2024, entry version 30.
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=SAMN05518801_11710 {ECO:0000313|EMBL:SFG32890.1};
OS Novosphingobium sp. CF614.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=1884364 {ECO:0000313|EMBL:SFG32890.1, ECO:0000313|Proteomes:UP000199304};
RN [1] {ECO:0000313|EMBL:SFG32890.1, ECO:0000313|Proteomes:UP000199304}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CF614 {ECO:0000313|EMBL:SFG32890.1,
RC ECO:0000313|Proteomes:UP000199304};
RA de Groot N.N.;
RL Submitted (OCT-2016) 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}.
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DR EMBL; FOOR01000017; SFG32890.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1I2QXU8; -.
DR STRING; 1884364.SAMN05518801_11710; -.
DR OrthoDB; 9804336at2; -.
DR UniPathway; UPA00056; UER00093.
DR Proteomes; UP000199304; 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_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 {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|ARBA:ARBA00022695, ECO:0000256|HAMAP-
KW Rule:MF_01520}; Reference proteome {ECO:0000313|Proteomes:UP000199304};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01520}.
FT DOMAIN 238..391
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT REGION 1..238
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT REGION 239..394
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 245..247
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 245
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
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 271..272
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 279
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 293..295
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 369..372
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 376
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 379
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 30
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 37
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 169
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 224
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 271
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 370
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
SQ SEQUENCE 394 AA; 40913 MW; 3DBA6D7A3FED9D1E CRC64;
MSRIVSEQEP GGRDARKVAA VVVAAGQGLR AGQPLPKQFA IWRGKPVVRH SVEALAAAGV
SPILVVIPQG AGSVARESLR DVPGVKFTDG GGTRQESVRL GLEVLAGADP DLVLIHDAAR
PLLPAAVIDR VLAALVHHKG AIPVLSVVDS LAHAEHGVRG EVMGAAARRE DLRRVQTPQA
FRFADILAAH RGWNGPTTAG DDARVAQAWG LEVAMVEGDE ALHKLTFAAD FAAPGPAVRV
GTGYDVHRLA AGKELWLCGV AIDHDQGLAG HSDADVAIHA LVDALLGAIG AGDIGQHFPP
GDPQWKSAAS HRFLSHAGAL VREAGYVLGN ADVTIICEAP KIGPHREAMR ARLAEILGVD
IAEISVKATT TEKLGFTGRG EGIAAQAIVS LSKA
//
