DPDS_MYCTU
ID DPDS_MYCTU Reviewed; 296 AA.
AC P9WFF7; L0T9E4; O05837; P60479;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 40.
DE RecName: Full=Decaprenyl diphosphate synthase;
DE Short=DecaPP;
DE EC=2.5.1.86;
DE EC=2.5.1.87;
DE AltName: Full=Decaprenyl pyrophosphate synthase;
DE AltName: Full=Long-chain isoprenyl diphosphate synthase;
DE AltName: Full=Trans,polycis-decaprenyl diphosphate synthase;
GN Name=uppS; OrderedLocusNames=Rv2361c; ORFNames=MTCY27.19;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION AS A DECAPRENYL DIPHOSPHATE SYNTHASE, CATALYTIC ACTIVITY,
RP SUBSTRATE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=11004176; DOI=10.1128/jb.182.20.5771-5778.2000;
RA Crick D.C., Schulbach M.C., Zink E.E., Macchia M., Barontini S.,
RA Besra G.S., Brennan P.J.;
RT "Polyprenyl phosphate biosynthesis in Mycobacterium tuberculosis and
RT Mycobacterium smegmatis.";
RL J. Bacteriol. 182:5771-5778(2000).
RN [3]
RP FUNCTION AS A DECAPRENYL DIPHOSPHATE SYNTHASE, SUBSTRATE SPECIFICITY, AND
RP SUBCELLULAR LOCATION.
RX PubMed=10816587; DOI=10.1074/jbc.m003194200;
RA Schulbach M.C., Brennan P.J., Crick D.C.;
RT "Identification of a short (C15) chain Z-isoprenyl diphosphate synthase and
RT a homologous long (C50) chain isoprenyl diphosphate synthase in
RT Mycobacterium tuberculosis.";
RL J. Biol. Chem. 275:22876-22881(2000).
RN [4]
RP FUNCTION AS A DECAPRENYL DIPHOSPHATE SYNTHASE, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, COFACTOR, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=15516568; DOI=10.1128/jb.186.22.7564-7570.2004;
RA Kaur D., Brennan P.J., Crick D.C.;
RT "Decaprenyl diphosphate synthesis in Mycobacterium tuberculosis.";
RL J. Bacteriol. 186:7564-7570(2004).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 13-296 IN COMPLEX WITH SUBSTRATE
RP ANALOGS, COFACTOR, AND SUBUNIT.
RX PubMed=18597781; DOI=10.1016/j.jmb.2008.05.060;
RA Wang W., Dong C., McNeil M., Kaur D., Mahapatra S., Crick D.C.,
RA Naismith J.H.;
RT "The structural basis of chain length control in Rv1086.";
RL J. Mol. Biol. 381:129-140(2008).
CC -!- FUNCTION: Catalyzes the sequential condensation of isopentenyl
CC diphosphate (IPP) in the cis configuration with (2Z,6E)-farnesyl
CC diphosphate (Z-FPP or EZ-FPP) generating the 50 carbon product
CC trans,polycis-decaprenyl diphosphate. When (2E,6E)-farnesyl diphosphate
CC (E-FPP or EE-FPP) is used in vitro, both primary products decaprenyl
CC diphosphate and (2E,6E,10E)-geranylgeranyl diphosphate (EEE-GGPP) are
CC synthesized. M.tuberculosis does not synthesize (2E,6E,10Z)-
CC geranylgeranyl diphosphate (EEZ-GGPP) and heptaprenyl diphosphate. Can
CC also accept many different allylic substrates, including E-geranyl
CC diphosphate (E-GPP), neryl diphosphate (NPP), and all-trans-geranyl-
CC geranyl diphosphate. {ECO:0000269|PubMed:10816587,
CC ECO:0000269|PubMed:11004176, ECO:0000269|PubMed:15516568}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate =
CC (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate + 7
CC diphosphate; Xref=Rhea:RHEA:47096, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:87356, ChEBI:CHEBI:128769, ChEBI:CHEBI:162247;
CC EC=2.5.1.86;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = di-
CC trans,poly-cis-polyprenyl diphosphate + n diphosphate;
CC Xref=Rhea:RHEA:53008, Rhea:RHEA-COMP:13431, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:128769, ChEBI:CHEBI:136960, ChEBI:CHEBI:175763;
CC EC=2.5.1.87;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15516568, ECO:0000269|PubMed:18597781};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15516568, ECO:0000269|PubMed:18597781};
CC Note=Binds 2 magnesium ions per subunit. Can also use manganese as
CC divalent cation, however calcium and zinc ions are much less effective.
CC {ECO:0000269|PubMed:15516568, ECO:0000269|PubMed:18597781};
CC -!- ACTIVITY REGULATION: Activated by dithiothreitol and inhibited by EDTA.
CC {ECO:0000269|PubMed:15516568}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=29 uM for NPP (at pH 7.9 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15516568};
CC KM=40 uM for EEE-GGPP (at pH 7.9 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15516568};
CC KM=84 uM for EE-FPP (at pH 7.9 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15516568};
CC KM=89 uM for IPP (at pH 7.9 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15516568};
CC KM=290 uM for EZ-FPP (at pH 7.9 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15516568};
CC KM=490 uM for E-GPP (at pH 7.9 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15516568};
CC Vmax=12 pmol/min/mg enzyme with EEE-GGPP as substrate (at pH 7.9 and
CC 37 degrees Celsius) {ECO:0000269|PubMed:15516568};
CC Vmax=21 pmol/min/mg enzyme with NPP as substrate (at pH 7.9 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15516568};
CC Vmax=25 pmol/min/mg enzyme with E-GPP as substrate (at pH 7.9 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15516568};
CC Vmax=30 pmol/min/mg enzyme with EE-FPP as substrate (at pH 7.9 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15516568};
CC Vmax=4800 pmol/min/mg enzyme with EZ-FPP as substrate (at pH 7.9 and
CC 37 degrees Celsius) {ECO:0000269|PubMed:15516568};
CC pH dependence:
CC Optimum pH is between 7.5 and 8.5. {ECO:0000269|PubMed:15516568};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18597781}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:10816587,
CC ECO:0000269|PubMed:11004176}.
CC -!- SIMILARITY: Belongs to the UPP synthase family. {ECO:0000305}.
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DR EMBL; AL123456; CCP45149.1; -; Genomic_DNA.
DR PIR; H70585; H70585.
DR RefSeq; NP_216877.1; NC_000962.3.
DR RefSeq; WP_003412212.1; NZ_NVQJ01000029.1.
DR PDB; 2VG2; X-ray; 1.95 A; A/B/C/D=13-296.
DR PDB; 2VG3; X-ray; 1.80 A; A/B/C/D=13-296.
DR PDB; 2VG4; X-ray; 2.60 A; A/B/C/D=13-296.
DR PDB; 4ONC; X-ray; 1.83 A; A/B=13-296.
DR PDB; 6IME; X-ray; 1.55 A; A/B=1-296.
DR PDBsum; 2VG2; -.
DR PDBsum; 2VG3; -.
DR PDBsum; 2VG4; -.
DR PDBsum; 4ONC; -.
DR PDBsum; 6IME; -.
DR AlphaFoldDB; P9WFF7; -.
DR SMR; P9WFF7; -.
DR STRING; 83332.Rv2361c; -.
DR DrugBank; DB02552; Geranyl Diphosphate.
DR DrugBank; DB04714; ISOPENTENYL PYROPHOSPHATE.
DR PaxDb; P9WFF7; -.
DR PRIDE; P9WFF7; -.
DR DNASU; 888964; -.
DR GeneID; 888964; -.
DR KEGG; mtu:Rv2361c; -.
DR TubercuList; Rv2361c; -.
DR eggNOG; COG0020; Bacteria.
DR OMA; PRTEGHK; -.
DR PhylomeDB; P9WFF7; -.
DR BioCyc; MetaCyc:G185E-6587-MON; -.
DR BRENDA; 2.5.1.86; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
DR GO; GO:0008834; F:di-trans,poly-cis-decaprenylcistransferase activity; IDA:MTBBASE.
DR GO; GO:0000287; F:magnesium ion binding; IDA:MTBBASE.
DR GO; GO:0030145; F:manganese ion binding; IDA:MTBBASE.
DR GO; GO:0002094; F:polyprenyltransferase activity; IBA:GO_Central.
DR GO; GO:0050347; F:trans-octaprenyltranstransferase activity; IDA:MTBBASE.
DR GO; GO:0033850; F:Z-farnesyl diphosphate synthase activity; IDA:MTBBASE.
DR GO; GO:0016094; P:polyprenol biosynthetic process; IDA:MTBBASE.
DR CDD; cd00475; Cis_IPPS; 1.
DR Gene3D; 3.40.1180.10; -; 1.
DR HAMAP; MF_01139; ISPT; 1.
DR InterPro; IPR001441; UPP_synth-like.
DR InterPro; IPR018520; UPP_synth-like_CS.
DR InterPro; IPR036424; UPP_synth-like_sf.
DR PANTHER; PTHR10291; PTHR10291; 1.
DR Pfam; PF01255; Prenyltransf; 1.
DR SUPFAM; SSF64005; SSF64005; 1.
DR TIGRFAMs; TIGR00055; uppS; 1.
DR PROSITE; PS01066; UPP_SYNTHASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Magnesium; Membrane; Metal-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..296
FT /note="Decaprenyl diphosphate synthase"
FT /id="PRO_0000123641"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 76
FT /evidence="ECO:0000250"
FT ACT_SITE 124
FT /note="Proton acceptor"
FT BINDING 76..80
FT /ligand="substrate"
FT BINDING 76
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 81
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 89
FT /ligand="substrate"
FT BINDING 93
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 121..124
FT /ligand="substrate"
FT BINDING 125
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 127
FT /ligand="substrate"
FT BINDING 168
FT /ligand="substrate"
FT BINDING 244
FT /ligand="substrate"
FT BINDING 250..252
FT /ligand="substrate"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 292..294
FT /ligand="substrate"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:2VG3"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 69..74
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 78..84
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 89..110
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 114..121
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 122..126
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 129..152
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 155..161
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 168..181
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 186..195
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 197..213
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 224..230
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 240..244
FT /evidence="ECO:0007829|PDB:6IME"
FT TURN 252..261
FT /evidence="ECO:0007829|PDB:6IME"
FT STRAND 263..266
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 271..273
FT /evidence="ECO:0007829|PDB:6IME"
FT HELIX 276..288
FT /evidence="ECO:0007829|PDB:6IME"
SQ SEQUENCE 296 AA; 33791 MW; 93895E54253615AA CRC64;
MARDARKRTS SNFPQLPPAP DDYPTFPDTS TWPVVFPELP AAPYGGPCRP PQHTSKAAAP
RIPADRLPNH VAIVMDGNGR WATQRGLART EGHKMGEAVV IDIACGAIEL GIKWLSLYAF
STENWKRSPE EVRFLMGFNR DVVRRRRDTL KKLGVRIRWV GSRPRLWRSV INELAVAEEM
TKSNDVITIN YCVNYGGRTE ITEATREIAR EVAAGRLNPE RITESTIARH LQRPDIPDVD
LFLRTSGEQR SSNFMLWQAA YAEYIFQDKL WPDYDRRDLW AACEEYASRT RRFGSA
