ISPF_SALTY
ID ISPF_SALTY Reviewed; 159 AA.
AC Q8ZMF7;
DT 15-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 117.
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=STM2929;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND MAGNESIUM IONS, COFACTOR, AND SUBUNIT.
RG Structural Genomics Of Infectious Diseases (CSGID);
RA Osipiuk J., Gu M., Peterson S., Anderson W.F., Joachimiak A.;
RT "2-c-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella
RT typhimurium.";
RL Submitted (MAR-2009) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND DIVALENT CATIONS, COFACTOR, AND SUBUNIT.
RG Seattle structural genomics center for infectious disease (SSGCID);
RA Staker B.L., Edwards T.E.;
RT "Crystal structure of 2-c-methyl-d-erythritol 2,4-cyclodiphos synthase from
RT Salmonella typhimurium bound to cytidine.";
RL Submitted (JUL-2011) to the PDB data bank.
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 -!- 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 -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00107, ECO:0000269|Ref.2,
CC ECO:0000269|Ref.3};
CC Note=Binds 1 divalent metal cation per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000269|Ref.2, ECO:0000269|Ref.3};
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|Ref.2, ECO:0000269|Ref.3}.
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; AE006468; AAL21809.1; -; Genomic_DNA.
DR RefSeq; NP_461850.1; NC_003197.2.
DR RefSeq; WP_001219245.1; NC_003197.2.
DR PDB; 3GHZ; X-ray; 2.03 A; A/B/C=1-159.
DR PDB; 3T80; X-ray; 2.50 A; A/B/C/D/E/F=1-159.
DR PDBsum; 3GHZ; -.
DR PDBsum; 3T80; -.
DR AlphaFoldDB; Q8ZMF7; -.
DR SMR; Q8ZMF7; -.
DR STRING; 99287.STM2929; -.
DR BindingDB; Q8ZMF7; -.
DR ChEMBL; CHEMBL4523930; -.
DR PaxDb; Q8ZMF7; -.
DR EnsemblBacteria; AAL21809; AAL21809; STM2929.
DR GeneID; 1254452; -.
DR KEGG; stm:STM2929; -.
DR PATRIC; fig|99287.12.peg.3083; -.
DR HOGENOM; CLU_084630_2_0_6; -.
DR OMA; QHFGTGR; -.
DR PhylomeDB; Q8ZMF7; -.
DR BioCyc; SENT99287:STM2929-MON; -.
DR UniPathway; UPA00056; UER00095.
DR EvolutionaryTrace; Q8ZMF7; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IBA:GO_Central.
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..159
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /id="PRO_0000189501"
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 /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 132..135
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 139
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 142
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 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 1..16
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 23..25
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 39..51
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 57..60
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 73..86
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 90..99
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 109..120
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:3GHZ"
FT HELIX 138..141
FT /evidence="ECO:0007829|PDB:3GHZ"
FT STRAND 144..155
FT /evidence="ECO:0007829|PDB:3GHZ"
SQ SEQUENCE 159 AA; 16900 MW; 9FD88D2C95662939 CRC64;
MRIGHGFDVH AFGGEGPIII GGVRIPYEKG LLAHSDGDVA LHALTDALLG AAALGDIGKL
FPDTDPAFKG ADSRELLREA WRRIQAKGYT LGNVDVTIIA QAPKMLPHIP QMRVFIAEDL
GCHMDEVNVK ATTTEKLGFT GRGEGIACEA VALLMKAAK
