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Bifunctional enzyme IspD/IspF [Includes: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) (MEP cytidylyltransferase) (MCT) (4-diphosphocytidyl-2C-methyl-D-erythritol synthase); 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (MECDP-synthase) (MECPP-synthase) (MECPS) (EC 4.6.1.12)]

 A0A147DBE3_9RHIZ        Unreviewed;       400 AA.
A0A147DBE3;
08-JUN-2016, integrated into UniProtKB/TrEMBL.
08-JUN-2016, sequence version 1.
28-MAR-2018, entry version 20.
RecName: Full=Bifunctional enzyme IspD/IspF {ECO:0000256|HAMAP-Rule:MF_01520};
Includes:
RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase {ECO:0000256|HAMAP-Rule:MF_01520};
EC=2.7.7.60 {ECO:0000256|HAMAP-Rule:MF_01520};
AltName: Full=MEP cytidylyltransferase {ECO:0000256|HAMAP-Rule:MF_01520};
Short=MCT {ECO:0000256|HAMAP-Rule:MF_01520};
AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase {ECO:0000256|HAMAP-Rule:MF_01520};
Includes:
RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase {ECO:0000256|HAMAP-Rule:MF_01520};
Short=MECDP-synthase {ECO:0000256|HAMAP-Rule:MF_01520};
Short=MECPP-synthase {ECO:0000256|HAMAP-Rule:MF_01520};
Short=MECPS {ECO:0000256|HAMAP-Rule:MF_01520};
EC=4.6.1.12 {ECO:0000256|HAMAP-Rule:MF_01520};
Name=ispDF {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000313|EMBL:KTR08497.1};
ORFNames=NS365_00705 {ECO:0000313|EMBL:KTR08497.1};
Aureimonas ureilytica.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
Aurantimonadaceae; Aureimonas.
NCBI_TaxID=401562 {ECO:0000313|EMBL:KTR08497.1, ECO:0000313|Proteomes:UP000078529};
[1] {ECO:0000313|EMBL:KTR08497.1, ECO:0000313|Proteomes:UP000078529}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=NS365 {ECO:0000313|EMBL:KTR08497.1,
ECO:0000313|Proteomes:UP000078529};
PubMed=26793183;
Midha S., Bansal K., Sharma S., Kumar N., Patil P.P., Chaudhry V.,
Patil P.B.;
"Genomic Resource of Rice Seed Associated Bacteria.";
Front. Microbiol. 6:1551-1551(2016).
-!- FUNCTION: Bifunctional enzyme that catalyzes the formation of 4-
diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-
D-erythritol 4-phosphate (MEP) (IspD), and catalyzes the
conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-
phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-
cyclodiphosphate (ME-CPP) with a corresponding release of cytidine
5-monophosphate (CMP) (IspF). {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00771987}.
-!- CATALYTIC ACTIVITY: 2-phospho-4-(cytidine 5'-diphospho)-2-C-
methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
+ CMP. {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00771955}.
-!- CATALYTIC ACTIVITY: CTP + 2-C-methyl-D-erythritol 4-phosphate =
diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.
{ECO:0000256|HAMAP-Rule:MF_01520, ECO:0000256|SAAS:SAAS00709147}.
-!- COFACTOR:
Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
Evidence={ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00771949};
-!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate
biosynthesis via DXP pathway; isopentenyl diphosphate from 1-
deoxy-D-xylulose 5-phosphate: step 2/6. {ECO:0000256|HAMAP-
Rule:MF_01520, ECO:0000256|SAAS:SAAS00709253}.
-!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate
biosynthesis via DXP pathway; isopentenyl diphosphate from 1-
deoxy-D-xylulose 5-phosphate: step 4/6. {ECO:0000256|HAMAP-
Rule:MF_01520, ECO:0000256|SAAS:SAAS00771963}.
-!- SIMILARITY: In the C-terminal section; belongs to the IspF family.
{ECO:0000256|HAMAP-Rule:MF_01520, ECO:0000256|SAAS:SAAS00771954}.
-!- SIMILARITY: In the N-terminal section; belongs to the IspD/TarI
cytidylyltransferase family. IspD subfamily. {ECO:0000256|HAMAP-
Rule:MF_01520, ECO:0000256|SAAS:SAAS00771938}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_01520}.
-!- CAUTION: The sequence shown here is derived from an
EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
preliminary data. {ECO:0000313|EMBL:KTR08497.1}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; LDQA01000001; KTR08497.1; -; Genomic_DNA.
RefSeq; WP_058598350.1; NZ_LDQA01000001.1.
EnsemblBacteria; KTR08497; KTR08497; NS365_00705.
PATRIC; fig|401562.4.peg.139; -.
UniPathway; UPA00056; UER00093.
UniPathway; UPA00056; UER00095.
Proteomes; UP000078529; Unassembled WGS sequence.
GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IEA:UniProtKB-UniRule.
GO; GO:0050518; F:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniPathway.
GO; GO:0016114; P:terpenoid biosynthetic process; IEA:UniProtKB-UniRule.
CDD; cd02516; CDP-ME_synthetase; 1.
CDD; cd00554; MECDP_synthase; 1.
Gene3D; 3.30.1330.50; -; 1.
Gene3D; 3.90.550.10; -; 1.
HAMAP; MF_00108; IspD; 1.
HAMAP; MF_01520; IspDF; 1.
HAMAP; MF_00107; IspF; 1.
InterPro; IPR001228; IspD.
InterPro; IPR026596; IspD/F.
InterPro; IPR034683; IspD/TarI.
InterPro; IPR018294; ISPD_synthase_CS.
InterPro; IPR003526; MECDP_synthase.
InterPro; IPR020555; MECDP_synthase_CS.
InterPro; IPR036571; MECDP_synthase_sf.
InterPro; IPR029044; Nucleotide-diphossugar_trans.
Pfam; PF01128; IspD; 1.
Pfam; PF02542; YgbB; 1.
SUPFAM; SSF53448; SSF53448; 1.
SUPFAM; SSF69765; SSF69765; 1.
TIGRFAMs; TIGR00453; ispD; 1.
TIGRFAMs; TIGR00151; ispF; 1.
PROSITE; PS01295; ISPD; 1.
PROSITE; PS01350; ISPF; 1.
3: Inferred from homology;
Complete proteome {ECO:0000313|Proteomes:UP000078529};
Isoprene biosynthesis {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00771928};
Lyase {ECO:0000256|HAMAP-Rule:MF_01520, ECO:0000256|SAAS:SAAS00771989,
ECO:0000313|EMBL:KTR08497.1};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00771962};
Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00771957};
Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00981526, ECO:0000313|EMBL:KTR08497.1};
Reference proteome {ECO:0000313|Proteomes:UP000078529};
Transferase {ECO:0000256|HAMAP-Rule:MF_01520,
ECO:0000256|SAAS:SAAS00981526, ECO:0000313|EMBL:KTR08497.1}.
DOMAIN 239 391 YgbB. {ECO:0000259|Pfam:PF02542}.
REGION 1 238 2-C-methyl-D-erythritol 4-phosphate
cytidylyltransferase. {ECO:0000256|HAMAP-
Rule:MF_01520}.
REGION 239 400 2-C-methyl-D-erythritol 2,4-
cyclodiphosphate synthase.
{ECO:0000256|HAMAP-Rule:MF_01520}.
REGION 245 247 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01520}.
REGION 271 272 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01520}.
REGION 275 283 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01520}.
REGION 293 295 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01520}.
REGION 368 372 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_01520}.
METAL 245 245 Divalent metal cation.
{ECO:0000256|HAMAP-Rule:MF_01520}.
METAL 247 247 Divalent metal cation.
{ECO:0000256|HAMAP-Rule:MF_01520}.
METAL 279 279 Divalent metal cation.
{ECO:0000256|HAMAP-Rule:MF_01520}.
BINDING 302 302 Substrate; via carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01520}.
BINDING 376 376 Substrate; via carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01520}.
BINDING 379 379 Substrate. {ECO:0000256|HAMAP-
Rule:MF_01520}.
SITE 18 18 Transition state stabilizer.
{ECO:0000256|HAMAP-Rule:MF_01520}.
SITE 27 27 Transition state stabilizer.
{ECO:0000256|HAMAP-Rule:MF_01520}.
SITE 158 158 Positions MEP for the nucleophilic
attack. {ECO:0000256|HAMAP-
Rule:MF_01520}.
SITE 215 215 Positions MEP for the nucleophilic
attack. {ECO:0000256|HAMAP-
Rule:MF_01520}.
SITE 271 271 Transition state stabilizer.
{ECO:0000256|HAMAP-Rule:MF_01520}.
SITE 370 370 Transition state stabilizer.
{ECO:0000256|HAMAP-Rule:MF_01520}.
SEQUENCE 400 AA; 42620 MW; 3C778FA5A3840EB2 CRC64;
MDQSKTAVVI VAAGRGERAG QSAEGPKQYR RIGGRPVLQW TVEAFLRFPM FQHIVVLIHP
DDVDRARDCL ASYGDRVRLV EGSITRQASV LKGLEALREA APHVVLVHDG VRPFVSERVI
ASVLDAVTER GGAIPSVPVT DTIKRMGDRG LIANTVDRRE LFAAQTPQGF PFGLILGAHE
AAVQQTALSF TDDASLFEWL GHPVALVPGE IGNVKLTLAE DIVAADNKLK GTSGMIDVRT
GNGYDVHQLV EGDHVTLCGV RIPHDQSLLG HSDADVGLHA LTDALLATCG AGDIGTHFPP
SDPQWKGAAS TLFLQHAVEI VRAKGGRVCN VDITLIAEAP KVGPHRAAMV ACISEVTGLD
NERVSIKATT NEMLGFIGRR EGIAAIATAS VVYGEAEERS


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