ID S5XTI3_PARAH Unreviewed; 301 AA.
AC S5XTI3;
DT 16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT 16-OCT-2013, sequence version 1.
DT 27-MAR-2024, entry version 60.
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=JCM7686_1386 {ECO:0000313|EMBL:AGT08487.1};
OS Paracoccus aminophilus JCM 7686.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Paracoccus.
OX NCBI_TaxID=1367847 {ECO:0000313|EMBL:AGT08487.1, ECO:0000313|Proteomes:UP000015480};
RN [1] {ECO:0000313|EMBL:AGT08487.1, ECO:0000313|Proteomes:UP000015480}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 7686 {ECO:0000313|EMBL:AGT08487.1};
RX PubMed=24517536; DOI=10.1186/1471-2164-15-124;
RA Dziewit L., Czarnecki J., Wibberg D., Radlinska M., Mrozek P., Szymczak M.,
RA Schluter A., Puhler A., Bartosik D.;
RT "Architecture and functions of a multipartite genome of the methylotrophic
RT bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary
RT chromids.";
RL BMC Genomics 15:124-124(2014).
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|ARBA:ARBA00008480,
CC ECO:0000256|HAMAP-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}.
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DR EMBL; CP006650; AGT08487.1; -; Genomic_DNA.
DR AlphaFoldDB; S5XTI3; -.
DR STRING; 1367847.JCM7686_1386; -.
DR KEGG; pami:JCM7686_1386; -.
DR PATRIC; fig|1367847.3.peg.1357; -.
DR eggNOG; COG0245; Bacteria.
DR eggNOG; COG1211; Bacteria.
DR HOGENOM; CLU_042800_0_0_5; -.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000015480; Chromosome.
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; 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; 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}; Nucleotidyltransferase {ECO:0000313|EMBL:AGT08487.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000015480};
KW Transferase {ECO:0000313|EMBL:AGT08487.1}.
FT DOMAIN 145..298
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT BINDING 152..154
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 152
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 154
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 178..179
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 186
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT BINDING 200..202
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 276..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 283
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 286
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 178
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
FT SITE 277
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00107"
SQ SEQUENCE 301 AA; 31561 MW; 71BC05449A141F04 CRC64;
MRAGLESLAG SGVTHVLIHD GARPLVSPEV IAGVVTALQE GARAAAPALA VTDALWRAED
GKVTGTADRE GLYRAQTPQG FALDAILAAH RAAPEGAADD VELARRAGLV VTVTEGSETN
LKLTWPQDFA RAEKILEQDM SITDIRLGNG FDVHAFGPGT HLWLCGVQIA HDKGLVGHSD
ADVGMHALTD AIYGALAEGD IGRHFPPSDA KWKGADSSIF LKHAVDLAAE KGFRLANADV
TLICEFPKIG PHASAMQQRL AEIMGLEPDR ISVKATTSER LGFTGRSEGI ASIATATLVI
G
//
