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Entry: A0A328AK98_9CAUL
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ID   A0A328AK98_9CAUL        Unreviewed;       381 AA.
AC   A0A328AK98;
DT   10-OCT-2018, integrated into UniProtKB/TrEMBL.
DT   10-OCT-2018, sequence version 1.
DT   24-JAN-2024, entry version 25.
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=DJ017_12765 {ECO:0000313|EMBL:RAK55322.1};
OS   Phenylobacterium soli.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Caulobacterales;
OC   Caulobacteraceae; Phenylobacterium.
OX   NCBI_TaxID=2170551 {ECO:0000313|EMBL:RAK55322.1, ECO:0000313|Proteomes:UP000249254};
RN   [1] {ECO:0000313|Proteomes:UP000249254}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LX32 {ECO:0000313|Proteomes:UP000249254};
RA   Li X.;
RL   Submitted (MAY-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|HAMAP-Rule:MF_01520};
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={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|HAMAP-Rule:MF_01520}.
CC   -!- SIMILARITY: Belongs to the IspD/TarI cytidylyltransferase family. IspD
CC       subfamily. {ECO:0000256|ARBA:ARBA00009789}.
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:RAK55322.1}.
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DR   EMBL; QFYQ01000001; RAK55322.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A328AK98; -.
DR   OrthoDB; 9804336at2; -.
DR   UniPathway; UPA00056; UER00093.
DR   Proteomes; UP000249254; 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; 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.
PE   3: Inferred from homology;
KW   Isoprene biosynthesis {ECO:0000256|ARBA:ARBA00023229, ECO:0000256|HAMAP-
KW   Rule:MF_01520}; Lyase {ECO:0000256|HAMAP-Rule:MF_01520};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_01520};
KW   Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_01520};
KW   Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695, ECO:0000256|HAMAP-
KW   Rule:MF_01520}; Reference proteome {ECO:0000313|Proteomes:UP000249254};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_01520}.
FT   DOMAIN          225..377
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000259|Pfam:PF02542"
FT   REGION          1..224
FT                   /note="2-C-methyl-D-erythritol 4-phosphate
FT                   cytidylyltransferase"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   REGION          225..381
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         231..233
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         231
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         233
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         257..258
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         265
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         279..281
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         355..358
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         362
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         365
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            15
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            22
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            149
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            204
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            257
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            356
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
SQ   SEQUENCE   381 AA;  40218 MW;  2B2D809778C2E830 CRC64;
     MSFSAVVVAA GSGLRAGPGE PKVWRTLGGK PIVRWSVEGL LSAGARDVVV VVARDRLGQV
     DEALVGLEGW KAVTGGRTRA ESVQAGLAAI SASRQQPVLI HDAARPFVTR EHVGRLLAAL
     DVADGAVPAL PVADTLKRGE GLIDETVPRA GLWRAQTPQA FRSGRLKAAY RRWPAGEEPT
     DDAAVVERAG GHVAMVPGDP MLMKLTYPED FFMAEQLAGA RRVVRTGFGV DAHRFGPGDV
     VWLCGIRIEH DLGLVGHSDA DCGLHALTDA VLGAIAAADI GEHFPPSDPR WKGASSDQFL
     AHAVSLVGAQ GGRILNADVT LICERPKIRP HRDAMRARIA ELLGLPVGRV SVKATTTEGM
     GFTGREEGLM AQAVVTVETP L
//
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