ISPF_BACSU
ID ISPF_BACSU Reviewed; 158 AA.
AC Q06756;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 03-AUG-2022, entry version 143.
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}; Synonyms=yacN;
GN OrderedLocusNames=BSU00910;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7510287; DOI=10.1016/s0021-9258(17)37310-6;
RA Gagnon Y., Breton R., Putzer H., Pelchat M., Grunberg-Manago M.,
RA Lapointe J.;
RT "Clustering and co-transcription of the Bacillus subtilis genes encoding
RT the aminoacyl-tRNA synthetases specific for glutamate and for cysteine and
RT the first enzyme for cysteine biosynthesis.";
RL J. Biol. Chem. 269:7473-7482(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=7584024; DOI=10.1093/dnares/1.1.1;
RA Ogasawara N., Nakai S., Yoshikawa H.;
RT "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis
RT chromosome containing the replication origin.";
RL DNA Res. 1:1-14(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP DISRUPTION PHENOTYPE.
RX PubMed=12270818; DOI=10.1128/jb.184.20.5609-5618.2002;
RA Campbell T.L., Brown E.D.;
RT "Characterization of the depletion of 2-C-methyl-D-erythritol-2,4-
RT cyclodiphosphate synthase in Escherichia coli and Bacillus subtilis.";
RL J. Bacteriol. 184:5609-5618(2002).
RN [5]
RP FUNCTION IN THE ISOPRENE BIOSYNTHESIS, AND DISRUPTION PHENOTYPE.
RX PubMed=17458547; DOI=10.1007/s00253-007-0953-5;
RA Julsing M.K., Rijpkema M., Woerdenbag H.J., Quax W.J., Kayser O.;
RT "Functional analysis of genes involved in the biosynthesis of isoprene in
RT Bacillus subtilis.";
RL Appl. Microbiol. Biotechnol. 75:1377-1384(2007).
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:17458547}.
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 Note=Binds 1 divalent metal cation per subunit. {ECO:0000255|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:0000255|HAMAP-Rule:MF_00107}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00107}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene reveal a loss of rod
CC shape, irregular septation, multicompartmentalized cells, and thickened
CC cell walls. It also induces a decrease in isoprene production.
CC {ECO:0000269|PubMed:12270818, ECO:0000269|PubMed:17458547}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000305}.
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DR EMBL; L14580; AAA21795.1; -; Genomic_DNA.
DR EMBL; D26185; BAA05325.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB11867.1; -; Genomic_DNA.
DR PIR; F69741; F69741.
DR RefSeq; NP_387972.1; NC_000964.3.
DR RefSeq; WP_003225745.1; NZ_JNCM01000029.1.
DR PDB; 5IWX; X-ray; 1.99 A; A/B/C/D/E/F=1-158.
DR PDB; 5IWY; X-ray; 1.99 A; A/B/C/D/E/F=1-158.
DR PDBsum; 5IWX; -.
DR PDBsum; 5IWY; -.
DR AlphaFoldDB; Q06756; -.
DR SMR; Q06756; -.
DR STRING; 224308.BSU00910; -.
DR PaxDb; Q06756; -.
DR PRIDE; Q06756; -.
DR EnsemblBacteria; CAB11867; CAB11867; BSU_00910.
DR GeneID; 64301929; -.
DR GeneID; 936634; -.
DR KEGG; bsu:BSU00910; -.
DR PATRIC; fig|224308.179.peg.92; -.
DR eggNOG; COG0245; Bacteria.
DR InParanoid; Q06756; -.
DR OMA; QHFGTGR; -.
DR PhylomeDB; Q06756; -.
DR BioCyc; BSUB:BSU00910-MON; -.
DR BRENDA; 4.6.1.12; 658.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000001570; 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..158
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /id="PRO_0000189441"
FT BINDING 9..11
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 9
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 11
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 35..36
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 43
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT BINDING 57..59
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 62..66
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 101..107
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 133..136
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 140
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 143
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 35
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT SITE 134
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00107"
FT STRAND 2..17
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:5IWX"
FT HELIX 40..52
FT /evidence="ECO:0007829|PDB:5IWX"
FT HELIX 58..61
FT /evidence="ECO:0007829|PDB:5IWX"
FT TURN 67..71
FT /evidence="ECO:0007829|PDB:5IWX"
FT HELIX 74..87
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 90..100
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:5IWX"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:5IWX"
FT HELIX 110..120
FT /evidence="ECO:0007829|PDB:5IWX"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 128..133
FT /evidence="ECO:0007829|PDB:5IWX"
FT HELIX 139..142
FT /evidence="ECO:0007829|PDB:5IWX"
FT STRAND 145..157
FT /evidence="ECO:0007829|PDB:5IWX"
SQ SEQUENCE 158 AA; 17126 MW; ED11D03EC3752BD0 CRC64;
MFRIGQGFDV HQLVEGRPLI IGGIEIPYEK GLLGHSDADV LLHTVADACL GAVGEGDIGK
HFPDTDPEFK DADSFKLLQH VWGIVKQKGY VLGNIDCTII AQKPKMLPYI EDMRKRIAEG
LEADVSQVNV KATTTEKLGF TGRAEGIAAQ ATVLIQKG
