ID A0A418WMZ6_9SPHN Unreviewed; 389 AA.
AC A0A418WMZ6;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 08-NOV-2023, entry version 19.
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=D3876_14880 {ECO:0000313|EMBL:RJF91379.1};
OS Sphingomonas cavernae.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=2320861 {ECO:0000313|EMBL:RJF91379.1, ECO:0000313|Proteomes:UP000286100};
RN [1] {ECO:0000313|EMBL:RJF91379.1, ECO:0000313|Proteomes:UP000286100}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K2R01-6 {ECO:0000313|EMBL:RJF91379.1,
RC ECO:0000313|Proteomes:UP000286100};
RA Zhu H.;
RL Submitted (SEP-2018) 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:RJF91379.1}.
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DR EMBL; QYUM01000003; RJF91379.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A418WMZ6; -.
DR OrthoDB; 9804336at2; -.
DR UniPathway; UPA00056; UER00093.
DR Proteomes; UP000286100; 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 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:UP000286100};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01520}.
FT DOMAIN 230..383
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT REGION 1..230
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT REGION 231..389
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 237..239
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 237
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 239
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 263..264
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 271
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 285..287
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 361..364
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 368
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
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 19
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 26
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 155
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 210
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 263
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 362
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
SQ SEQUENCE 389 AA; 40758 MW; 7C77BC8B9DF6E390 CRC64;
MKSGFHNVAL IVAAGKGERA GAARPKQFAL LGGKPVVAHS IDAALTHPAI DGVIVVTAAD
QRQAMEVALD GRDVRAIVDG GASRRESVLA GLEAISALGG AVRVLIHDAA RPLLPHAVID
RLLAQLDGSA GAVPVLPVAD TLATADEALG DIVPRTGLVR VQTPQAFRFD AILAAHRLWP
VDQEATDDAQ ILRAVELEVA MVEGDSMLEK ITHPQDFASA EARLAARASI RTAMGYDVHR
LVAGEELWLG GVLIPHDKGL SGHSDADVAL HALTDALLGT IGAGDIGMHF PPSDPQWRGA
SSDRFLEHAA ALVAEARGSI EHVDLTIICE APKIGPYRDA MRNRIAALLR VDMARVSIKA
TTTERLGFTG RGEGIAAQAV ATVRISGDI
//
