Decaprenyl diphosphate synthase - Mycobacterium tuberculosis

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P60479 (DPDS_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 69. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Decaprenyl diphosphate synthase
Short name=DecaPP
EC=2.5.1.86
EC=2.5.1.87

Alternative name(s):
Decaprenyl pyrophosphate synthase
Long-chain isoprenyl diphosphate synthase
Trans,polycis-decaprenyl diphosphate synthase

Gene names

Name:	uppS
Ordered Locus Names:	Rv2361c, MT2430
ORF Names:	MTCY27.19

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	296 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) in the cis configuration with (2Z,6E)-farnesyl diphosphate (Z-FPP or EZ-FPP) generating the 50 carbon product trans,polycis-decaprenyl diphosphate. When (2E,6E)-farnesyl diphosphate (E-FPP or EE-FPP) is used in vitro, both primary products decaprenyl diphosphate and (2E,6E,10E)-geranylgeranyl diphosphate (EEE-GGPP) are synthesized. M.tuberculosis does not synthesize (2E,6E,10Z)-geranylgeranyl diphosphate (EEZ-GGPP) and heptaprenyl diphosphate. Can also accept many different allylic substrates, including E-geranyl diphosphate (E-GPP), neryl diphosphate (NPP), and all-trans-geranyl-geranyl diphosphate. Ref.3 Ref.4 Ref.5
Catalytic activity	(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate. Ref.3 Ref.5 (2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55). Ref.3 Ref.5
Cofactor	Binds 2 magnesium ions per subunit. Can also use manganese as divalent cation, however calcium and zinc ions are much less effective. Ref.5 Ref.6
Enzyme regulation	Activated by dithiothreitol and inhibited by EDTA. Ref.5
Subunit structure	Homodimer. Ref.6
Subcellular location	Cell membrane Ref.3 Ref.4.
Sequence similarities	Belongs to the UPP synthase family.
Biophysicochemical properties	Kinetic parameters: K_M=29 µM for NPP (at pH 7.9 and 37 degrees Celsius) Ref.5 K_M=40 µM for EEE-GGPP (at pH 7.9 and 37 degrees Celsius) K_M=84 µM for EE-FPP (at pH 7.9 and 37 degrees Celsius) K_M=89 µM for IPP (at pH 7.9 and 37 degrees Celsius) K_M=290 µM for EZ-FPP (at pH 7.9 and 37 degrees Celsius) K_M=490 µM for E-GPP (at pH 7.9 and 37 degrees Celsius) V_max=12 pmol/min/mg enzyme with EEE-GGPP as substrate (at pH 7.9 and 37 degrees Celsius) V_max=21 pmol/min/mg enzyme with NPP as substrate (at pH 7.9 and 37 degrees Celsius) V_max=25 pmol/min/mg enzyme with E-GPP as substrate (at pH 7.9 and 37 degrees Celsius) V_max=30 pmol/min/mg enzyme with EE-FPP as substrate (at pH 7.9 and 37 degrees Celsius) V_max=4800 pmol/min/mg enzyme with EZ-FPP as substrate (at pH 7.9 and 37 degrees Celsius) pH dependence: Optimum pH is between 7.5 and 8.5.

Ontologies

Keywords
Cellular component	Cell membrane Membrane
Ligand	Magnesium Metal-binding
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	growth Inferred from mutant phenotype PubMed 12657046. Source: MTBBASE polyprenol biosynthetic process Inferred from direct assay Ref.4. Source: MTBBASE
Cellular_component	cytosol Inferred from direct assay Ref.4. Source: MTBBASE plasma membrane Inferred from direct assay Ref.4 PubMed 15525680. Source: MTBBASE
Molecular_function	Z-farnesyl diphosphate synthase activity Inferred from direct assay Ref.5. Source: MTBBASE di-trans,poly-cis-decaprenylcistransferase activity Inferred from direct assay Ref.4. Source: MTBBASE magnesium ion binding Inferred from direct assay Ref.5. Source: MTBBASE manganese ion binding Inferred from direct assay Ref.5. Source: MTBBASE trans-octaprenyltranstransferase activity Inferred from direct assay Ref.5. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 296

296

Decaprenyl diphosphate synthase HAMAP-Rule MF_01139

PRO_0000123641

Regions

Region

76 – 80

Substrate binding HAMAP-Rule MF_01139

Region

121 – 124

Substrate binding HAMAP-Rule MF_01139

Region

250 – 252

Substrate binding HAMAP-Rule MF_01139

Region

292 – 294

Substrate binding HAMAP-Rule MF_01139

Sites

Active site

By similarity

Active site

124

Proton acceptor

Metal binding

Magnesium By similarity

Metal binding

263

Magnesium By similarity

Binding site

Substrate By similarity

Binding site

Substrate

Binding site

Substrate By similarity

Binding site

125

Substrate By similarity

Binding site

127

Substrate

Binding site

168

Substrate

Binding site

244

Substrate

Secondary structure

296

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P60479 [UniParc].

Last modified February 16, 2004. Version 1.
Checksum: 93895E54253615AA
Show »

FASTA

296

33,791

        10         20         30         40         50         60 
MARDARKRTS SNFPQLPPAP DDYPTFPDTS TWPVVFPELP AAPYGGPCRP PQHTSKAAAP 

        70         80         90        100        110        120 
RIPADRLPNH VAIVMDGNGR WATQRGLART EGHKMGEAVV IDIACGAIEL GIKWLSLYAF 

       130        140        150        160        170        180 
STENWKRSPE EVRFLMGFNR DVVRRRRDTL KKLGVRIRWV GSRPRLWRSV INELAVAEEM 

       190        200        210        220        230        240 
TKSNDVITIN YCVNYGGRTE ITEATREIAR EVAAGRLNPE RITESTIARH LQRPDIPDVD 

       250        260        270        280        290 
LFLRTSGEQR SSNFMLWQAA YAEYIFQDKL WPDYDRRDLW AACEEYASRT RRFGSA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. Barrell B.G. Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"Polyprenyl phosphate biosynthesis in Mycobacterium tuberculosis and Mycobacterium smegmatis." Crick D.C., Schulbach M.C., Zink E.E., Macchia M., Barontini S., Besra G.S., Brennan P.J. J. Bacteriol. 182:5771-5778(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A DECAPRENYL DIPHOSPHATE SYNTHASE, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION.
[4]	"Identification of a short (C15) chain Z-isoprenyl diphosphate synthase and a homologous long (C50) chain isoprenyl diphosphate synthase in Mycobacterium tuberculosis." Schulbach M.C., Brennan P.J., Crick D.C. J. Biol. Chem. 275:22876-22881(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A DECAPRENYL DIPHOSPHATE SYNTHASE, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION.
[5]	"Decaprenyl diphosphate synthesis in Mycobacterium tuberculosis." Kaur D., Brennan P.J., Crick D.C. J. Bacteriol. 186:7564-7570(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A DECAPRENYL DIPHOSPHATE SYNTHASE, CATALYTIC ACTIVITY, ENZYME REGULATION, COFACTOR, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
[6]	"The structural basis of chain length control in Rv1086." Wang W., Dong C., McNeil M., Kaur D., Mahapatra S., Crick D.C., Naismith J.H. J. Mol. Biol. 381:129-140(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 13-296 IN COMPLEX WITH SUBSTRATE ANALOGS, COFACTOR, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842579 Genomic DNA. Translation: CAB08462.1.
AE000516 Genomic DNA. Translation: AAK46724.1.
AL123456 Genomic DNA. Translation: CCP45149.1.

PIR

H70585.

RefSeq

NP_216877.1. NC_000962.3.
NP_336910.1. NC_002755.2.
YP_006515795.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2VG2	X-ray	1.95	A/B/C/D	13-296	[»]
2VG3	X-ray	1.80	A/B/C/D	13-296	[»]
2VG4	X-ray	2.60	A/B/C/D	13-296	[»]

ProteinModelPortal

P60479.

SMR

P60479. Positions 13-296.

ModBase

Search...

Protein-protein interaction databases

STRING

83332.Rv2361c.

Proteomic databases

PRIDE

P60479.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK46724; AAK46724; MT2430.

GeneID

13319067.
888964.
925908.

KEGG

mtc:MT2430.
mtu:Rv2361c.
mtv:RVBD_2361c.

PATRIC

18127094. VBIMycTub22151_2655.

Organism-specific databases

TubercuList

Rv2361c.

Phylogenomic databases

eggNOG

COG0020.

HOGENOM

HOG000006055.

K14215.

OMA

ETLRWCK.

ProtClustDB

PRK14827.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-15221.

Family and domain databases

Gene3D

3.40.1180.10. 1 hit.

HAMAP

MF_01139. ISPT.

InterPro

IPR001441. UPP_synth-like.
IPR018520. UPP_synth-like_CS.
[Graphical view]

PANTHER

PTHR10291. PTHR10291. 1 hit.

Pfam

PF01255. Prenyltransf. 1 hit.
[Graphical view]

SUPFAM

SSF64005. UPP_synth. 1 hit.

TIGRFAMs

TIGR00055. uppS. 1 hit.

PROSITE

PS01066. UPP_SYNTHASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P60479.

Entry information

Entry name

DPDS_MYCTU

Accession

Primary (citable) accession number: P60479
Secondary accession number(s): L0T9E4, O05837

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 16, 2004
Last sequence update:	February 16, 2004
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents