ID R6GKZ1_9FIRM Unreviewed; 374 AA.
AC R6GKZ1;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 24-JAN-2024, entry version 53.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {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|HAMAP-Rule:MF_00107};
GN Name=ispF {ECO:0000256|HAMAP-Rule:MF_00107};
GN ORFNames=BN704_00738 {ECO:0000313|EMBL:CDB26138.1};
OS Firmicutes bacterium CAG:552.
OC Bacteria; Bacillota.
OX NCBI_TaxID=1263029 {ECO:0000313|EMBL:CDB26138.1, ECO:0000313|Proteomes:UP000018403};
RN [1] {ECO:0000313|EMBL:CDB26138.1, ECO:0000313|Proteomes:UP000018403}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MGS:552 {ECO:0000313|Proteomes:UP000018403};
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) to the EMBL/GenBank/DDBJ databases.
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=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};
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};
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 2/6. {ECO:0000256|ARBA:ARBA00004787}.
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 IspD/TarI cytidylyltransferase family. IspD
CC subfamily. {ECO:0000256|ARBA:ARBA00009789}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000256|HAMAP-
CC Rule:MF_00107}.
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:CDB26138.1}.
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DR EMBL; CBDH010000046; CDB26138.1; -; Genomic_DNA.
DR AlphaFoldDB; R6GKZ1; -.
DR STRING; 1263029.BN704_00738; -.
DR UniPathway; UPA00056; UER00093.
DR Proteomes; UP000018403; 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-EC.
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; IPR001228; IspD.
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_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}; Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Reference proteome {ECO:0000313|Proteomes:UP000018403};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 218..369
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT BINDING 224..226
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 224
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 226
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 250..251
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 258
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 272..274
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 347..350
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 250
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT SITE 348
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
SQ SEQUENCE 374 AA; 40180 MW; 2C5BABE7EEB0AE94 CRC64;
MKSTDAVILC AGKGARAKTA KNKVLCYFGA KTAIEYCLDA FAPFCNSLIV VAAEDDIDEI
KEISAPYSAT VTVGGATRFL SVLNGLKKAT SPTVIIHDAA RPFVTKEIIE KCIKSAETHG
SGIAATPTVD TIKRVENGMI VKNIKRDGLY NVQTPQAFDT KKIVDAYLKA AENPNSLYTD
DSAVFAAYGY APVIVESDPS NKKITTPQDI IALPPCQKIG NGIDFHRLVP KRKLILGGVE
IPNKKGLLGH SDADVLTHAV MDALLSAIGM PDIGVLFPST EQYKNANSLE LLDEVMRYVS
EAKYSIMSVS AVVIAKEPKL SPFMTNIRQT LAERMNLELH QINVSATTTE GMGVIGQGDG
MAATAVCLLN RTEK
//
