ID A0A2T8HTG9_9RHOB Unreviewed; 395 AA.
AC A0A2T8HTG9;
DT 18-JUL-2018, integrated into UniProtKB/TrEMBL.
DT 18-JUL-2018, sequence version 1.
DT 24-JAN-2024, entry version 26.
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=DDE20_11285 {ECO:0000313|EMBL:PVH28754.1};
OS Pararhodobacter oceanensis.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Pararhodobacter.
OX NCBI_TaxID=2172121 {ECO:0000313|EMBL:PVH28754.1, ECO:0000313|Proteomes:UP000245911};
RN [1] {ECO:0000313|EMBL:PVH28754.1, ECO:0000313|Proteomes:UP000245911}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AM505 {ECO:0000313|EMBL:PVH28754.1,
RC ECO:0000313|Proteomes:UP000245911};
RA Wang X.-L., Du Z.-J.;
RT "Pararhodobacter oceanense sp. nov., isolated from marine intertidal
RT sediment.";
RL Submitted (APR-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:PVH28754.1}.
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DR EMBL; QDKM01000004; PVH28754.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2T8HTG9; -.
DR OrthoDB; 9804336at2; -.
DR UniPathway; UPA00056; UER00093.
DR Proteomes; UP000245911; 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:UP000245911};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01520}.
FT DOMAIN 239..392
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT REGION 1..239
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT REGION 240..395
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 246..248
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 246
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 248
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 272..273
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 280
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 294..296
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 370..373
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 377
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 380
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 149
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 202
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 272
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 371
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
SQ SEQUENCE 395 AA; 42159 MW; 3466839C721B40C2 CRC64;
MRNAENTAVV IVAAGRGSRM GGGMPKQWRQ LAGKPVIAHT VAAFQDAGFA RICLVIHPED
AGLAAGLPVS LVHGGATRSD SVRAALEHLA QDPPARVLIH DAARPLVPRA VIAEVMEALD
TQSAAAPALP VTDALWRGGD GVVMGTQARD GLFRAQTPQG FRFAAILSAH RALKHDAADD
VEVIRAAGEE VWITQGSDEN LKLTYPIDFT RAERILSERQ TIKGQTFSGQ ALEGSKMDIR
LGNGFDVHAF TEGDHLWLCG HKIAHERGLL GHSDADVGMH ALTDAIYGAL AQGDIGRHFP
PSDPQWKGAA SHIFLRHAVE LAAEMGYRIA NIDVTLICER PKITPHADAM RAALGEIMGL
EIERISVKAS TSERLGFTGR EEGIAAITSA TLVKP
//
