ID A0A367YXW0_9ACTN Unreviewed; 374 AA.
AC A0A367YXW0;
DT 07-NOV-2018, integrated into UniProtKB/TrEMBL.
DT 07-NOV-2018, sequence version 1.
DT 27-MAR-2024, entry version 23.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000256|ARBA:ARBA00012579, ECO:0000256|HAMAP-Rule:MF_00107};
DE Short=MECDP-synthase {ECO:0000256|HAMAP-Rule:MF_00107};
DE Short=MECPP-synthase {ECO:0000256|HAMAP-Rule:MF_00107};
DE Short=MECPS {ECO:0000256|HAMAP-Rule:MF_00107};
DE EC=4.6.1.12 {ECO:0000256|ARBA:ARBA00012579, ECO:0000256|HAMAP-Rule:MF_00107};
GN Name=ispF {ECO:0000256|HAMAP-Rule:MF_00107};
GN ORFNames=DT076_04455 {ECO:0000313|EMBL:RCK70670.1};
OS Desertihabitans brevis.
OC Bacteria; Actinomycetota; Actinomycetes; Propionibacteriales;
OC Propionibacteriaceae; Desertihabitans.
OX NCBI_TaxID=2268447 {ECO:0000313|EMBL:RCK70670.1, ECO:0000313|Proteomes:UP000252770};
RN [1] {ECO:0000313|EMBL:RCK70670.1, ECO:0000313|Proteomes:UP000252770}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=16Sb5-5 {ECO:0000313|EMBL:RCK70670.1,
RC ECO:0000313|Proteomes:UP000252770};
RA Liu S.;
RT "Desertimonas flava gen. nov. sp. nov.";
RL Submitted (JUL-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-
CC erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).
CC {ECO:0000256|ARBA:ARBA00002459}.
CC -!- FUNCTION: Involved in the biosynthesis of isopentenyl diphosphate (IPP)
CC and dimethylallyl diphosphate (DMAPP), two major building blocks of
CC isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-
CC C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol
CC 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine
CC 5-monophosphate (CMP). {ECO:0000256|HAMAP-Rule:MF_00107}.
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_00107, ECO:0000256|RuleBase:RU004395};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00107};
CC Note=Binds 1 divalent metal cation per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_00107};
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_00107}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000256|HAMAP-Rule:MF_00107}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000256|HAMAP-
CC Rule:MF_00107, ECO:0000256|RuleBase:RU004395}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00107}.
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:RCK70670.1}.
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DR EMBL; QOUI01000002; RCK70670.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A367YXW0; -.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000252770; Unassembled WGS sequence.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0070567; F:cytidylyltransferase activity; IEA:InterPro.
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_00107; IspF; 1.
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; TIGR00151; ispF; 1.
DR PANTHER; PTHR32125; 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC; 1.
DR PANTHER; PTHR32125:SF4; 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, 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_00107};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_00107};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00107}; Reference proteome {ECO:0000313|Proteomes:UP000252770}.
FT DOMAIN 222..372
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT BINDING 228..230
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 228
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 230
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 255..256
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 263
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 277..279
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 350..353
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 360
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT SITE 255
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT SITE 351
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
SQ SEQUENCE 374 AA; 38518 MW; B063CA7809030A18 CRC64;
MGAGSPAKAL RLLAGRPLVW HSVAALVEGG ADEVVVAIRP ELVEQFSAAL ADLAERVPLR
FVPGGRERQE SVDAALDALT TGPRTSRPPA VVLVHDAARP LVPPEVVRRV ADRVLAGDPV
VVPVVPVVDT VRRLDESGST GVDRSRLRAV QTPQGFRPDV LREGHDRLRA DGTTVTDDAG
ACELAGHRAV LVEGSPRSLK VTTEHDLQLA EGLLGAAAAT LRTGTGIDVH RLAPGRPMRV
ACLDFPDEEM GPVGHSDGDV VAHAACDALL AAAGLGDLGS NYGTSDPAWA GASGRAFLVE
TARRLAAAGF HPVNVSVQLV GQRPRFAARR AEAEAVMGAA LGAPVSLSAT TTDGLGLTGR
GEGLAAIATA LVRG
//
