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ISPDF_DINSH
ID   ISPDF_DINSH             Reviewed;         400 AA.
AC   A8LKV5;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   04-DEC-2007, sequence version 1.
DT   03-AUG-2022, entry version 85.
DE   RecName: Full=Bifunctional enzyme IspD/IspF {ECO:0000255|HAMAP-Rule:MF_01520};
DE   Includes:
DE     RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              EC=2.7.7.60 {ECO:0000255|HAMAP-Rule:MF_01520};
DE     AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE     AltName: Full=MEP cytidylyltransferase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MCT {ECO:0000255|HAMAP-Rule:MF_01520};
DE   Includes:
DE     RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MECDP-synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MECPP-synthase {ECO:0000255|HAMAP-Rule:MF_01520};
DE              Short=MECPS {ECO:0000255|HAMAP-Rule:MF_01520};
DE              EC=4.6.1.12 {ECO:0000255|HAMAP-Rule:MF_01520};
GN   Name=ispDF {ECO:0000255|HAMAP-Rule:MF_01520}; OrderedLocusNames=Dshi_1577;
OS   Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC   Roseobacteraceae; Dinoroseobacter.
OX   NCBI_TaxID=398580;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 16493 / NCIMB 14021 / DFL 12;
RX   PubMed=19741735; DOI=10.1038/ismej.2009.94;
RA   Wagner-Dobler I., Ballhausen B., Berger M., Brinkhoff T., Buchholz I.,
RA   Bunk B., Cypionka H., Daniel R., Drepper T., Gerdts G., Hahnke S., Han C.,
RA   Jahn D., Kalhoefer D., Kiss H., Klenk H.P., Kyrpides N., Liebl W.,
RA   Liesegang H., Meincke L., Pati A., Petersen J., Piekarski T.,
RA   Pommerenke C., Pradella S., Pukall R., Rabus R., Stackebrandt E., Thole S.,
RA   Thompson L., Tielen P., Tomasch J., von Jan M., Wanphrut N., Wichels A.,
RA   Zech H., Simon M.;
RT   "The complete genome sequence of the algal symbiont Dinoroseobacter shibae:
RT   a hitchhiker's guide to life in the sea.";
RL   ISME J. 4:61-77(2010).
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:0000255|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:0000255|HAMAP-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:0000255|HAMAP-Rule:MF_01520};
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={ECO:0000255|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:0000255|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 4/6. {ECO:0000255|HAMAP-Rule:MF_01520}.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the IspD/TarI
CC       cytidylyltransferase family. IspD subfamily. {ECO:0000255|HAMAP-
CC       Rule:MF_01520}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the IspF family.
CC       {ECO:0000255|HAMAP-Rule:MF_01520}.
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DR   EMBL; CP000830; ABV93319.1; -; Genomic_DNA.
DR   AlphaFoldDB; A8LKV5; -.
DR   SMR; A8LKV5; -.
DR   STRING; 398580.Dshi_1577; -.
DR   EnsemblBacteria; ABV93319; ABV93319; Dshi_1577.
DR   KEGG; dsh:Dshi_1577; -.
DR   eggNOG; COG0245; Bacteria.
DR   eggNOG; COG1211; Bacteria.
DR   HOGENOM; CLU_042800_2_3_5; -.
DR   OMA; TGYDVHA; -.
DR   UniPathway; UPA00056; UER00093.
DR   UniPathway; UPA00056; UER00095.
DR   Proteomes; UP000006833; Chromosome.
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; -; 1.
DR   Gene3D; 3.90.550.10; -; 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   PANTHER; PTHR43181; PTHR43181; 1.
DR   Pfam; PF01128; IspD; 1.
DR   Pfam; PF02542; YgbB; 1.
DR   SUPFAM; SSF53448; SSF53448; 1.
DR   SUPFAM; SSF69765; SSF69765; 1.
DR   TIGRFAMs; TIGR00453; ispD; 1.
DR   TIGRFAMs; TIGR00151; ispF; 1.
DR   PROSITE; PS01295; ISPD; 1.
DR   PROSITE; PS01350; ISPF; 1.
PE   3: Inferred from homology;
KW   Isoprene biosynthesis; Lyase; Metal-binding; Multifunctional enzyme;
KW   Nucleotidyltransferase; Reference proteome; Transferase.
FT   CHAIN           1..400
FT                   /note="Bifunctional enzyme IspD/IspF"
FT                   /id="PRO_0000333305"
FT   REGION          1..244
FT                   /note="2-C-methyl-D-erythritol 4-phosphate
FT                   cytidylyltransferase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   REGION          245..400
FT                   /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT                   synthase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         251..253
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         251
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         253
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         277..278
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         285
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         299..301
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         375..378
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         382
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   BINDING         385
FT                   /ligand="4-CDP-2-C-methyl-D-erythritol 2-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:57919"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            35
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            42
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            169
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            222
FT                   /note="Positions MEP for the nucleophilic attack"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            277
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
FT   SITE            376
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01520"
SQ   SEQUENCE   400 AA;  42011 MW;  23F281F018DD6475 CRC64;
     MSHRVLGTER ISPREEHVLT PNVTAILVAA GRGTRAGGGL AKQWRPLGAR RVIDWTLAAF
     DRATQVSELL VVLHPEDMDL AATLTAAKPL RCVSGGATRS ASVACALAAV ADPEAIVLIH
     DAARPVVSAD LIARVVAGVI ETGAAAPALP VVDALWTGAG DRVTGMQPRD GLYRAQTPQG
     FHAGAIRDAH AAATGAAADD VEIARAAGMP VAIVAGDEQN FKITYPQDFA RAAALLKERD
     KMDIRTGNGY DVHRFGTGDA VILCGVEVPH DRALMGHSDA DVGMHAVTDA IYGALGDGDI
     GQHFPPSDPQ WKGAASEIFL RHAVALAAER GYTITHMDCT LVCERPKIGP YHAVMKAKMS
     ELMGLQPDQV SVKATTSERL GFTGREEGIA ALATVTLVRT
 
 
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