ISPF_BURP1
ID ISPF_BURP1 Reviewed; 162 AA.
AC Q3JRA0;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 94.
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};
GN OrderedLocusNames=BURPS1710b_2511;
OS Burkholderia pseudomallei (strain 1710b).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; pseudomallei group.
OX NCBI_TaxID=320372;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1710b;
RX PubMed=20333227; DOI=10.1093/gbe/evq003;
RA Losada L., Ronning C.M., DeShazer D., Woods D., Fedorova N., Kim H.S.,
RA Shabalina S.A., Pearson T.R., Brinkac L., Tan P., Nandi T., Crabtree J.,
RA Badger J., Beckstrom-Sternberg S., Saqib M., Schutzer S.E., Keim P.,
RA Nierman W.C.;
RT "Continuing evolution of Burkholderia mallei through genome reduction and
RT large-scale rearrangements.";
RL Genome Biol. Evol. 2:102-116(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND ZINC IONS, COFACTOR, AND SUBUNIT.
RG Seattle structural genomics center for infectious disease (SSGCID);
RT "Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate
RT synthase from Burkholderia pseudomallei with hydrolyzed CDP.";
RL Submitted (OCT-2008) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND ZINC IONS, COFACTOR, AND SUBUNIT.
RG Seattle Structural Genomics Center for Infectious Disease (SSGCID);
RA Edwards T.E., Davies D.R., Hartley R., Zeller W.;
RT "Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
RT from Burkholderia pseudomallei in complex with a fragment-nucleoside fusion
RT D000161829.";
RL Submitted (OCT-2009) to the PDB data bank.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND ZINC IONS, COFACTOR, AND SUBUNIT.
RX PubMed=21359640; DOI=10.1007/s10969-011-9102-6;
RA Begley D.W., Hartley R.C., Davies D.R., Edwards T.E., Leonard J.T.,
RA Abendroth J., Burris C.A., Bhandari J., Myler P.J., Staker B.L.,
RA Stewart L.J.;
RT "Leveraging structure determination with fragment screening for infectious
RT disease drug targets: MECP synthase from Burkholderia pseudomallei.";
RL J. Struct. Funct. Genomics 12:63-76(2011).
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,
CC ECO:0000269|PubMed:21359640, ECO:0000269|Ref.2, ECO:0000269|Ref.3};
CC Note=Binds 1 divalent metal cation per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000269|PubMed:21359640, ECO:0000269|Ref.2,
CC 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|PubMed:21359640, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000255|HAMAP-
CC Rule:MF_00107}.
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DR EMBL; CP000124; ABA47450.1; -; Genomic_DNA.
DR RefSeq; WP_004191369.1; NC_007434.1.
DR PDB; 3F0D; X-ray; 1.20 A; A/B/C/D/E/F=1-162.
DR PDB; 3F0E; X-ray; 2.05 A; A/B/C=1-162.
DR PDB; 3F0F; X-ray; 2.09 A; A/B/C=1-162.
DR PDB; 3F0G; X-ray; 2.08 A; A/B/C/D/E/F=1-162.
DR PDB; 3IEQ; X-ray; 2.10 A; A/B/C=1-162.
DR PDB; 3JVH; X-ray; 1.69 A; A/B/C=1-162.
DR PDB; 3K14; X-ray; 1.70 A; A/B/C=1-162.
DR PDB; 3K2X; X-ray; 1.85 A; A/B/C=1-162.
DR PDB; 3KE1; X-ray; 2.05 A; A/B/C=1-162.
DR PDB; 3MBM; X-ray; 1.80 A; A/B/C=1-162.
DR PDB; 3P0Z; X-ray; 1.95 A; A/B/C=1-162.
DR PDB; 3P10; X-ray; 1.70 A; A/B/C=1-162.
DR PDB; 3QHD; X-ray; 1.70 A; A/B/C=1-162.
DR PDB; 6MWF; X-ray; 1.75 A; A/B/C=1-162.
DR PDB; 6MWI; X-ray; 1.75 A; A/B/C=1-162.
DR PDB; 6MWJ; X-ray; 2.05 A; A/B/C=1-162.
DR PDB; 6MWK; X-ray; 1.80 A; A/B/C=1-162.
DR PDB; 6NMO; X-ray; 1.45 A; A/B/C=1-162.
DR PDB; 6V3M; X-ray; 1.55 A; A/B/C=1-162.
DR PDBsum; 3F0D; -.
DR PDBsum; 3F0E; -.
DR PDBsum; 3F0F; -.
DR PDBsum; 3F0G; -.
DR PDBsum; 3IEQ; -.
DR PDBsum; 3JVH; -.
DR PDBsum; 3K14; -.
DR PDBsum; 3K2X; -.
DR PDBsum; 3KE1; -.
DR PDBsum; 3MBM; -.
DR PDBsum; 3P0Z; -.
DR PDBsum; 3P10; -.
DR PDBsum; 3QHD; -.
DR PDBsum; 6MWF; -.
DR PDBsum; 6MWI; -.
DR PDBsum; 6MWJ; -.
DR PDBsum; 6MWK; -.
DR PDBsum; 6NMO; -.
DR PDBsum; 6V3M; -.
DR AlphaFoldDB; Q3JRA0; -.
DR SMR; Q3JRA0; -.
DR EnsemblBacteria; ABA47450; ABA47450; BURPS1710b_2511.
DR GeneID; 56595885; -.
DR KEGG; bpm:BURPS1710b_2511; -.
DR HOGENOM; CLU_084630_2_0_4; -.
DR OMA; QHFGTGR; -.
DR OrthoDB; 1716560at2; -.
DR UniPathway; UPA00056; UER00095.
DR EvolutionaryTrace; Q3JRA0; -.
DR Proteomes; UP000002700; Chromosome I.
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.
FT CHAIN 1..162
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /id="PRO_0000237710"
FT BINDING 10..12
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 10
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 12
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 36..37
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 40..48
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 44
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 58..60
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 63..67
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 102..108
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 133..137
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
FT BINDING 144
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 36
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT SITE 135
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT STRAND 3..16
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 20..22
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 41..53
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:6NMO"
FT HELIX 75..88
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 91..101
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 111..122
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:3F0D"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:3F0D"
FT STRAND 146..158
FT /evidence="ECO:0007829|PDB:3F0D"
SQ SEQUENCE 162 AA; 17175 MW; 77F4A6B473C5961C CRC64;
MDFRIGQGYD VHQLVPGRPL IIGGVTIPYE RGLLGHSDAD VLLHAITDAL FGAAALGDIG
RHFSDTDPRF KGADSRALLR ECASRVAQAG FAIRNVDSTI IAQAPKLAPH IDAMRANIAA
DLDLPLDRVN VKAKTNEKLG YLGRGEGIEA QAAALVVREA AA
