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Database: UniProt
Entry: H3KE08_9BURK
LinkDB: H3KE08_9BURK
Original site: H3KE08_9BURK 
ID   H3KE08_9BURK            Unreviewed;       398 AA.
AC   H3KE08;
DT   18-APR-2012, integrated into UniProtKB/TrEMBL.
DT   18-APR-2012, sequence version 1.
DT   24-JAN-2024, entry version 78.
DE   RecName: Full=Bifunctional enzyme IspD/IspF {ECO:0000256|HAMAP-Rule:MF_01520};
DE   Includes:
DE     RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase {ECO:0000256|HAMAP-Rule:MF_01520};
DE              EC=2.7.7.60 {ECO:0000256|HAMAP-Rule:MF_01520};
DE     AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase {ECO:0000256|HAMAP-Rule:MF_01520};
DE     AltName: Full=MEP cytidylyltransferase {ECO:0000256|HAMAP-Rule:MF_01520};
DE              Short=MCT {ECO:0000256|HAMAP-Rule:MF_01520};
DE   Includes:
DE     RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000256|HAMAP-Rule:MF_01520};
DE              Short=MECDP-synthase {ECO:0000256|HAMAP-Rule:MF_01520};
DE              Short=MECPP-synthase {ECO:0000256|HAMAP-Rule:MF_01520};
DE              Short=MECPS {ECO:0000256|HAMAP-Rule:MF_01520};
DE              EC=4.6.1.12 {ECO:0000256|HAMAP-Rule:MF_01520};
GN   Name=ispDF {ECO:0000256|HAMAP-Rule:MF_01520};
GN   ORFNames=HMPREF9440_00969 {ECO:0000313|EMBL:EHY31652.1};
OS   Sutterella parvirubra YIT 11816.
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Sutterellaceae; Sutterella.
OX   NCBI_TaxID=762967 {ECO:0000313|EMBL:EHY31652.1, ECO:0000313|Proteomes:UP000004956};
RN   [1] {ECO:0000313|EMBL:EHY31652.1, ECO:0000313|Proteomes:UP000004956}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=YIT 11816 {ECO:0000313|EMBL:EHY31652.1,
RC   ECO:0000313|Proteomes:UP000004956};
RA   Weinstock G., Sodergren E., Clifton S., Fulton L., Fulton B., Courtney L.,
RA   Fronick C., Harrison M., Strong C., Farmer C., Delahaunty K., Markovic C.,
RA   Hall O., Minx P., Tomlinson C., Mitreva M., Hou S., Chen J., Wollam A.,
RA   Pepin K.H., Johnson M., Bhonagiri V., Zhang X., Suruliraj S., Warren W.,
RA   Chinwalla A., Mardis E.R., Wilson R.K.;
RL   Submitted (NOV-2011) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Bifunctional enzyme that catalyzes the formation of 4-
CC       diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-
CC       erythritol 4-phosphate (MEP) (IspD), and catalyzes the conversion of 4-
CC       diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-
CC       methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding
CC       release of cytidine 5-monophosphate (CMP) (IspF). {ECO:0000256|HAMAP-
CC       Rule:MF_01520}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-
CC         methyl-D-erythritol + diphosphate; Xref=Rhea:RHEA:13429,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, ChEBI:CHEBI:37563,
CC         ChEBI:CHEBI:57823, ChEBI:CHEBI:58262; EC=2.7.7.60;
CC         Evidence={ECO:0000256|ARBA:ARBA00001282, ECO:0000256|HAMAP-
CC         Rule:MF_01520};
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:0000256|ARBA:ARBA00000200, ECO:0000256|HAMAP-
CC         Rule:MF_01520};
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={ECO:0000256|ARBA:ARBA00001968,
CC         ECO:0000256|HAMAP-Rule:MF_01520};
CC   -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC       via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC       phosphate: step 2/6. {ECO:0000256|ARBA:ARBA00004787, ECO:0000256|HAMAP-
CC       Rule:MF_01520}.
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:0000256|ARBA:ARBA00004709, ECO:0000256|HAMAP-
CC       Rule:MF_01520}.
CC   -!- SIMILARITY: Belongs to the IspD/TarI cytidylyltransferase family. IspD
CC       subfamily. {ECO:0000256|ARBA:ARBA00009789}.
CC   -!- SIMILARITY: Belongs to the IspF family.
CC       {ECO:0000256|ARBA:ARBA00008480}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the IspF family.
CC       {ECO:0000256|HAMAP-Rule:MF_01520}.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the IspD/TarI
CC       cytidylyltransferase family. IspD subfamily. {ECO:0000256|HAMAP-
CC       Rule:MF_01520}.
CC   -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {ECO:0000256|HAMAP-Rule:MF_01520}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:EHY31652.1}.
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DR   EMBL; AFBQ01000131; EHY31652.1; -; Genomic_DNA.
DR   AlphaFoldDB; H3KE08; -.
DR   STRING; 762967.HMPREF9440_00969; -.
DR   PATRIC; fig|762967.3.peg.771; -.
DR   HOGENOM; CLU_042800_2_4_4; -.
DR   OrthoDB; 9806837at2; -.
DR   UniPathway; UPA00056; UER00093.
DR   Proteomes; UP000004956; Unassembled WGS sequence.
DR   GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0050518; F:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 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; cd02516; CDP-ME_synthetase; 1.
DR   CDD; cd00554; MECDP_synthase; 1.
DR   Gene3D; 3.30.1330.50; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; 1.
DR   HAMAP; MF_00108; IspD; 1.
DR   HAMAP; MF_01520; IspDF; 1.
DR   HAMAP; MF_00107; IspF; 1.
DR   InterPro; IPR001228; IspD.
DR   InterPro; IPR026596; IspD/F.
DR   InterPro; IPR034683; IspD/TarI.
DR   InterPro; IPR018294; ISPD_synthase_CS.
DR   InterPro; IPR003526; MECDP_synthase.
DR   InterPro; IPR020555; MECDP_synthase_CS.
DR   InterPro; IPR036571; MECDP_synthase_sf.
DR   InterPro; IPR029044; Nucleotide-diphossugar_trans.
DR   NCBIfam; TIGR00453; ispD; 1.
DR   NCBIfam; TIGR00151; ispF; 1.
DR   PANTHER; PTHR43181; 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC; 1.
DR   PANTHER; PTHR43181:SF1; 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC; 1.
DR   Pfam; PF01128; IspD; 1.
DR   Pfam; PF02542; YgbB; 1.
DR   SUPFAM; SSF69765; IpsF-like; 1.
DR   SUPFAM; SSF53448; Nucleotide-diphospho-sugar transferases; 1.
DR   PROSITE; PS01295; ISPD; 1.
DR   PROSITE; PS01350; ISPF; 1.
PE   3: Inferred from homology;
KW   Isoprene biosynthesis {ECO:0000256|ARBA:ARBA00023229, ECO:0000256|HAMAP-
KW   Rule:MF_01520};
KW   Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_01520};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_01520};
KW   Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268, ECO:0000256|HAMAP-
KW   Rule:MF_01520};
KW   Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695, ECO:0000256|HAMAP-
KW   Rule:MF_01520}; Reference proteome {ECO:0000313|Proteomes:UP000004956};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_01520}.
FT   DOMAIN          242..395
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000259|Pfam:PF02542"
FT   REGION          1..242
FT                   /note="2-C-methyl-D-erythritol 4-phosphate
FT                   cytidylyltransferase"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   REGION          243..398
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         249..251
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         249
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         251
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         275..276
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         283
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         297..299
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   BINDING         383
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            23
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            30
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            164
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            220
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            275
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT   SITE            374
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
SQ   SEQUENCE   398 AA;  42202 MW;  B5C3680B313B8636 CRC64;
     METPAMTSVR MTALVCAAGV GARMGLDRPK QYLRLGSRTM LEHTVHAIAS VERVDDVVVV
     VSAEDAYVDE AAAHFPAKAR VLKVGGATRA ETVQNGIAAA GWPADAWVLV HDAARPCLRA
     AEVDHLIDEV LGDDAVAGGI LALPMTDTVK RTDERRRILE TVPRKDLWRA ATPQLFRAGV
     LSEALSAAQA AGAELTDEAS AVEHLGLAVK VVSGRPTNLK VTHPGDERIA GLILGDAAVM
     PIRVGQGYDS HRLVEGRPLI LGGIEIPFEK GLDGHSDADV LLHAVTDAVL GAAALGDIGR
     HFPPSDPKWK GADSGKLLEA VVRLAKEKGW SVVNADATLV CERPKIAPHA EKMRGNVARL
     LGVSPEVVNL KAKTNEKMDD VGREAGMMAH AVVLMCRM
//
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