ISPF_THET8
ID ISPF_THET8 Reviewed; 152 AA.
AC Q8RQP5; Q5SHE0;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000255|HAMAP-Rule:MF_00107};
DE Short=MECDP-synthase {ECO:0000255|HAMAP-Rule:MF_00107};
DE Short=MECPP-synthase {ECO:0000255|HAMAP-Rule:MF_00107};
DE Short=MECPS {ECO:0000255|HAMAP-Rule:MF_00107};
DE EC=4.6.1.12 {ECO:0000255|HAMAP-Rule:MF_00107};
GN Name=ispF {ECO:0000255|HAMAP-Rule:MF_00107}; OrderedLocusNames=TTHA1790;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Kishida H., Wada T., Unzai S., Kuzuyama T., Terada T., Shirouzu M.,
RA Yokoyama S., Tame J.R.H., Park S.-Y.;
RT "2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Thermus
RT thermophilus HB8.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.52 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND MAGNESIUM IONS, FUNCTION AS A MECDP-SYNTHASE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
RX PubMed=12499535; DOI=10.1107/s0907444902017705;
RA Kishida H., Wada T., Unzai S., Kuzuyama T., Takagi M., Terada T.,
RA Shirouzu M., Yokoyama S., Tame J.R.H., Park S.-Y.;
RT "Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-
RT cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway
RT of isoprenoid synthesis.";
RL Acta Crystallogr. D 59:23-31(2003).
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:0000255|HAMAP-Rule:MF_00107,
CC ECO:0000269|PubMed:12499535}.
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:0000255|HAMAP-Rule:MF_00107,
CC ECO:0000269|PubMed:12499535};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00107,
CC ECO:0000269|PubMed:12499535};
CC Note=Binds 1 divalent metal cation per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000269|PubMed:12499535};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Thermostable. {ECO:0000269|PubMed:12499535};
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:0000255|HAMAP-Rule:MF_00107}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00107,
CC ECO:0000269|PubMed:12499535}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB082126; BAB86885.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD71613.1; -; Genomic_DNA.
DR RefSeq; WP_011228919.1; NC_006461.1.
DR RefSeq; YP_145056.1; NC_006461.1.
DR PDB; 1IV1; X-ray; 1.65 A; A/B/C/D/E/F=1-152.
DR PDB; 1IV2; X-ray; 1.55 A; A/B/C/D/E/F=1-152.
DR PDB; 1IV3; X-ray; 1.52 A; A/B/C/D/E/F=1-152.
DR PDB; 1IV4; X-ray; 1.55 A; A/B/C/D/E/F=1-152.
DR PDBsum; 1IV1; -.
DR PDBsum; 1IV2; -.
DR PDBsum; 1IV3; -.
DR PDBsum; 1IV4; -.
DR AlphaFoldDB; Q8RQP5; -.
DR SMR; Q8RQP5; -.
DR STRING; 300852.55773172; -.
DR DrugBank; DB04555; Cytidine-5'-Diphosphate.
DR DrugBank; DB03403; Cytidine-5'-Monophosphate.
DR EnsemblBacteria; BAD71613; BAD71613; BAD71613.
DR GeneID; 3169480; -.
DR KEGG; ttj:TTHA1790; -.
DR PATRIC; fig|300852.9.peg.1761; -.
DR eggNOG; COG0245; Bacteria.
DR HOGENOM; CLU_084630_2_1_0; -.
DR OMA; QHFGTGR; -.
DR PhylomeDB; Q8RQP5; -.
DR BRENDA; 4.6.1.12; 2305.
DR UniPathway; UPA00056; UER00095.
DR EvolutionaryTrace; Q8RQP5; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 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; cd00554; MECDP_synthase; 1.
DR Gene3D; 3.30.1330.50; -; 1.
DR HAMAP; MF_00107; IspF; 1.
DR InterPro; IPR003526; MECDP_synthase.
DR InterPro; IPR020555; MECDP_synthase_CS.
DR InterPro; IPR036571; MECDP_synthase_sf.
DR PANTHER; PTHR43181; PTHR43181; 1.
DR Pfam; PF02542; YgbB; 1.
DR SUPFAM; SSF69765; SSF69765; 1.
DR TIGRFAMs; TIGR00151; ispF; 1.
DR PROSITE; PS01350; ISPF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isoprene biosynthesis; Lyase; Metal-binding;
KW Reference proteome.
FT CHAIN 1..152
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /id="PRO_0000189511"
FT BINDING 8..10
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 8
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 10
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 34..35
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 42
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 56..58
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 61..65
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 100..106
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 131..135
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT SITE 34
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT SITE 133
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT STRAND 3..14
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 23..25
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 28..31
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:1IV3"
FT HELIX 39..50
FT /evidence="ECO:0007829|PDB:1IV3"
FT TURN 51..53
FT /evidence="ECO:0007829|PDB:1IV3"
FT HELIX 57..60
FT /evidence="ECO:0007829|PDB:1IV3"
FT TURN 66..70
FT /evidence="ECO:0007829|PDB:1IV3"
FT HELIX 73..86
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 91..99
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:1IV3"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:1IV3"
FT HELIX 109..120
FT /evidence="ECO:0007829|PDB:1IV3"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:1IV3"
FT STRAND 141..150
FT /evidence="ECO:0007829|PDB:1IV3"
SQ SEQUENCE 152 AA; 16520 MW; 0114C0E440DC28F3 CRC64;
MRIGYGEDSH RLEEGRPLYL CGLLIPSPVG ALAHSDGDAA LHALTDALLS AYGLGDIGLL
FPDTDPRWRG ERSEVFLREA LRLVEARGAK LLQASLVLTL DRPKLGPHRK ALVDSLSRLL
RLPQDRIGLT FKTSEGLAPS HVQARAVVLL DG
