ISPF_HAEIN
ID ISPF_HAEIN Reviewed; 158 AA.
AC P44815;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 140.
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=HI_0671;
OS Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=71421;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=7542800; DOI=10.1126/science.7542800;
RA Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
RA Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
RA McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
RA Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F.,
RA Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R.,
RA Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D.,
RA Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A.,
RA Small K.V., Fraser C.M., Smith H.O., Venter J.C.;
RT "Whole-genome random sequencing and assembly of Haemophilus influenzae
RT Rd.";
RL Science 269:496-512(1995).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=9719565; DOI=10.1002/elps.1150191046;
RA Fountoulakis M., Juranville J.-F., Roeder D., Evers S., Berndt P.,
RA Langen H.;
RT "Reference map of the low molecular mass proteins of Haemophilus
RT influenzae.";
RL Electrophoresis 19:1819-1827(1998).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH COBALT IONS, AND
RP SUBUNIT.
RX PubMed=12211023; DOI=10.1002/prot.10182;
RA Lehmann C., Lim K., Toedt J., Krajewski W., Howard A., Eisenstein E.,
RA Herzberg O.;
RT "Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase from
RT Haemophilus influenzae: activation by conformational transition.";
RL Proteins 49:135-138(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 2-158 IN COMPLEX WITH SUBSTRATE
RP ANALOGS AND MANGANESE IONS, COFACTOR, AND SUBUNIT.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
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:16021622};
CC Note=Binds 1 divalent metal cation per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000269|PubMed:16021622};
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:12211023, ECO:0000269|PubMed:16021622}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000255|HAMAP-
CC Rule:MF_00107, ECO:0000305}.
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DR EMBL; L42023; AAC22331.1; -; Genomic_DNA.
DR PIR; F64156; F64156.
DR RefSeq; NP_438831.1; NC_000907.1.
DR RefSeq; WP_005687916.1; NC_000907.1.
DR PDB; 1JN1; X-ray; 2.90 A; A/B/C=1-158.
DR PDB; 1VH8; X-ray; 2.35 A; A/B/C/D/E/F=2-158.
DR PDB; 1VHA; X-ray; 2.35 A; A/B/C/D/E/F=2-158.
DR PDB; 5ESV; X-ray; 3.10 A; E/F/G=2-13, E/F/G=38-158.
DR PDB; 5ESZ; X-ray; 4.19 A; C/G=2-14, C/G=38-158.
DR PDBsum; 1JN1; -.
DR PDBsum; 1VH8; -.
DR PDBsum; 1VHA; -.
DR PDBsum; 5ESV; -.
DR PDBsum; 5ESZ; -.
DR AlphaFoldDB; P44815; -.
DR SMR; P44815; -.
DR STRING; 71421.HI_0671; -.
DR EnsemblBacteria; AAC22331; AAC22331; HI_0671.
DR KEGG; hin:HI_0671; -.
DR PATRIC; fig|71421.8.peg.701; -.
DR eggNOG; COG0245; Bacteria.
DR HOGENOM; CLU_084630_2_0_6; -.
DR OMA; QHFGTGR; -.
DR PhylomeDB; P44815; -.
DR BioCyc; HINF71421:G1GJ1-706-MON; -.
DR BRENDA; 4.6.1.12; 2529.
DR UniPathway; UPA00056; UER00095.
DR EvolutionaryTrace; P44815; -.
DR Proteomes; UP000000579; 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_0000189472"
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 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..143
FT /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT /ligand_id="ChEBI:CHEBI:57919"
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..12
FT /evidence="ECO:0007829|PDB:1VH8"
FT STRAND 14..21
FT /evidence="ECO:0007829|PDB:1VH8"
FT STRAND 24..32
FT /evidence="ECO:0007829|PDB:1VH8"
FT HELIX 40..52
FT /evidence="ECO:0007829|PDB:1VH8"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:1VH8"
FT HELIX 64..67
FT /evidence="ECO:0007829|PDB:1JN1"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:1JN1"
FT HELIX 74..87
FT /evidence="ECO:0007829|PDB:1VH8"
FT STRAND 90..100
FT /evidence="ECO:0007829|PDB:1VH8"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:1JN1"
FT HELIX 107..120
FT /evidence="ECO:0007829|PDB:1VH8"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:1VH8"
FT STRAND 128..133
FT /evidence="ECO:0007829|PDB:1VH8"
FT HELIX 139..142
FT /evidence="ECO:0007829|PDB:1VH8"
FT STRAND 145..157
FT /evidence="ECO:0007829|PDB:1VH8"
SQ SEQUENCE 158 AA; 17194 MW; DC34BF347DEC2EFF CRC64;
MIRIGHGFDV HAFGEDRPLI IGGVEVPYHT GFIAHSDGDV ALHALTDAIL GAAALGDIGK
LFPDTDMQYK NADSRGLLRE AFRQVQEKGY KIGNVDITII AQAPKMRPHI DAMRAKIAED
LQCDIEQVNV KATTTEKLGF TGRQEGIACE AVALLIRQ
