ID A0A1B9N823_9MICO Unreviewed; 413 AA.
AC A0A1B9N823;
DT 02-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2016, sequence version 1.
DT 27-MAR-2024, entry version 44.
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=A7J15_10995 {ECO:0000313|EMBL:OCG72749.1}, E3O41_10235
GN {ECO:0000313|EMBL:QBR74735.1};
OS Microbacterium sediminis.
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae;
OC Microbacterium.
OX NCBI_TaxID=904291 {ECO:0000313|EMBL:OCG72749.1, ECO:0000313|Proteomes:UP000093355};
RN [1] {ECO:0000313|EMBL:OCG72749.1, ECO:0000313|Proteomes:UP000093355}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YLB-01 {ECO:0000313|EMBL:OCG72749.1,
RC ECO:0000313|Proteomes:UP000093355};
RA Lavstsen T., Jespersen J.S.;
RL Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:QBR74735.1, ECO:0000313|Proteomes:UP000295661}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YLB-01 {ECO:0000313|EMBL:QBR74735.1,
RC ECO:0000313|Proteomes:UP000295661};
RA Yu L.;
RL Submitted (MAR-2019) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:QBR74735.1, ECO:0000313|Proteomes:UP000295661}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YLB-01 {ECO:0000313|EMBL:QBR74735.1,
RC ECO:0000313|Proteomes:UP000295661};
RA Xu X.;
RT "Genomic analysis of Microbacterium sediminis YLB-01 reveals backgrounds
RT related to its deep sea enviroment adaptation.";
RL Submitted (APR-2019) 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 -!- FUNCTION: Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-
CC erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).
CC {ECO:0000256|ARBA:ARBA00002459}.
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: 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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; LXMD01000029; OCG72749.1; -; Genomic_DNA.
DR EMBL; CP038256; QBR74735.1; -; Genomic_DNA.
DR RefSeq; WP_067027892.1; NZ_KV744789.1.
DR AlphaFoldDB; A0A1B9N823; -.
DR STRING; 904291.A7J15_10995; -.
DR KEGG; msed:E3O41_10235; -.
DR OrthoDB; 9802561at2; -.
DR UniPathway; UPA00056; UER00093.
DR Proteomes; UP000093355; Unassembled WGS sequence.
DR Proteomes; UP000295661; 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; 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; PTHR32125; 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC; 1.
DR PANTHER; PTHR32125:SF4; 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, 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}; Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_01520};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695, ECO:0000256|HAMAP-
KW Rule:MF_01520}; Reference proteome {ECO:0000313|Proteomes:UP000093355};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01520}.
FT DOMAIN 260..410
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000259|Pfam:PF02542"
FT REGION 1..259
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT REGION 260..413
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 266..268
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 266
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 268
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 292..293
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 300
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT BINDING 314..316
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 388..391
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 395
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 398
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 27
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 34
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 167
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 292
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
FT SITE 389
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01520"
SQ SEQUENCE 413 AA; 41815 MW; DF3C21BA8C44AD8A CRC64;
MTQTQPSAPP LAPRIAAIVV AAGSGTRLGA GAPKAFVGLD AHTILRHALR GVFAGPLAQV
IVVAPQDRVG EALTDAREAA GDRAPLVSVV AGGASRQESV AAGLARVLPE IEIVLVHDAA
RALTPPAVFE RVVEAIDRTG WGAVPVLPVI DTIKRVEGER IVGVVDRSEL GAAQTPQGFR
RDVLEAAYAA AEREYTDDAA LVADAGHPIA AVDGDPLGFK ITTPADLERA RTLVAGDPIA
PVGPAARDAA GDARPAGPPR VGVGTDAHAF GGEGTLWLAG LEWPGEPALA GHSDGDAVAH
AIVDALLSAT GLGDIGSRFG TDRPELAGAH AEAFLAETAR LVREAGWEIG NVSVQVQAQR
PRFAARRAEA EAALSAALGG APVSVSATTT DGLGFTGRAE GVQALAVALV VPV
//
