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Protein

Decaprenyl diphosphate synthase

Gene

uppS

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.3 Publications

Catalytic activityi

(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate.
(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55).

Cofactori

Mg2+2 Publications, Mn2+2 PublicationsNote: Binds 2 magnesium ions per subunit. Can also use manganese as divalent cation, however calcium and zinc ions are much less effective.2 Publications

Enzyme regulationi

Activated by dithiothreitol and inhibited by EDTA.1 Publication

Kineticsi

  1. KM=29 µM for NPP (at pH 7.9 and 37 degrees Celsius)1 Publication
  2. KM=40 µM for EEE-GGPP (at pH 7.9 and 37 degrees Celsius)1 Publication
  3. KM=84 µM for EE-FPP (at pH 7.9 and 37 degrees Celsius)1 Publication
  4. KM=89 µM for IPP (at pH 7.9 and 37 degrees Celsius)1 Publication
  5. KM=290 µM for EZ-FPP (at pH 7.9 and 37 degrees Celsius)1 Publication
  6. KM=490 µM for E-GPP (at pH 7.9 and 37 degrees Celsius)1 Publication
  1. Vmax=12 pmol/min/mg enzyme with EEE-GGPP as substrate (at pH 7.9 and 37 degrees Celsius)1 Publication
  2. Vmax=21 pmol/min/mg enzyme with NPP as substrate (at pH 7.9 and 37 degrees Celsius)1 Publication
  3. Vmax=25 pmol/min/mg enzyme with E-GPP as substrate (at pH 7.9 and 37 degrees Celsius)1 Publication
  4. Vmax=30 pmol/min/mg enzyme with EE-FPP as substrate (at pH 7.9 and 37 degrees Celsius)1 Publication
  5. Vmax=4800 pmol/min/mg enzyme with EZ-FPP as substrate (at pH 7.9 and 37 degrees Celsius)1 Publication

pH dependencei

Optimum pH is between 7.5 and 8.5.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei76By similarity1
Metal bindingi76MagnesiumBy similarity1
Binding sitei81SubstrateBy similarity1
Binding sitei89Substrate1
Binding sitei93SubstrateBy similarity1
Active sitei124Proton acceptor1
Binding sitei125SubstrateBy similarity1
Binding sitei127Substrate1
Binding sitei168Substrate1
Binding sitei244Substrate1
Metal bindingi263MagnesiumBy similarity1

GO - Molecular functioni

  • di-trans,poly-cis-decaprenylcistransferase activity Source: MTBBASE
  • magnesium ion binding Source: MTBBASE
  • manganese ion binding Source: MTBBASE
  • polyprenyltransferase activity Source: GO_Central
  • trans-octaprenyltranstransferase activity Source: MTBBASE
  • Z-farnesyl diphosphate synthase activity Source: MTBBASE

GO - Biological processi

  • growth Source: MTBBASE
  • polyprenol biosynthetic process Source: MTBBASE
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-6587-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Decaprenyl diphosphate synthase (EC:2.5.1.86, EC:2.5.1.87)
Short name:
DecaPP
Alternative name(s):
Decaprenyl pyrophosphate synthase
Long-chain isoprenyl diphosphate synthase
Trans,polycis-decaprenyl diphosphate synthase
Gene namesi
Name:uppS
Ordered Locus Names:Rv2361c
ORF Names:MTCY27.19
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv2361c.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: MTBBASE
  • plasma membrane Source: MTBBASE
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001236411 – 296Decaprenyl diphosphate synthaseAdd BLAST296

Proteomic databases

PaxDbiP9WFF7.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi83332.Rv2361c.

Structurei

Secondary structure

1296
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi31 – 33Combined sources3
Beta strandi43 – 46Combined sources4
Turni64 – 66Combined sources3
Beta strandi69 – 74Combined sources6
Helixi78 – 84Combined sources7
Helixi89 – 110Combined sources22
Beta strandi114 – 121Combined sources8
Helixi124 – 126Combined sources3
Helixi129 – 152Combined sources24
Beta strandi155 – 161Combined sources7
Helixi168 – 181Combined sources14
Beta strandi186 – 195Combined sources10
Helixi197 – 213Combined sources17
Helixi219 – 221Combined sources3
Helixi224 – 230Combined sources7
Beta strandi231 – 233Combined sources3
Beta strandi240 – 244Combined sources5
Turni252 – 261Combined sources10
Beta strandi263 – 266Combined sources4
Helixi271 – 273Combined sources3
Helixi276 – 288Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2VG2X-ray1.95A/B/C/D13-296[»]
2VG3X-ray1.80A/B/C/D13-296[»]
2VG4X-ray2.60A/B/C/D13-296[»]
4ONCX-ray1.83A/B13-296[»]
ProteinModelPortaliP9WFF7.
SMRiP9WFF7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 80Substrate binding5
Regioni121 – 124Substrate binding4
Regioni250 – 252Substrate binding3
Regioni292 – 294Substrate binding3

Sequence similaritiesi

Belongs to the UPP synthase family.Curated

Phylogenomic databases

eggNOGiENOG4105CR3. Bacteria.
COG0020. LUCA.
KOiK14215.
OMAiWNRPKLE.
PhylomeDBiP9WFF7.

Family and domain databases

CDDicd00475. Cis_IPPS. 1 hit.
Gene3Di3.40.1180.10. 1 hit.
HAMAPiMF_01139. ISPT. 1 hit.
InterProiIPR001441. UPP_synth-like.
IPR018520. UPP_synth-like_CS.
[Graphical view]
PANTHERiPTHR10291. PTHR10291. 1 hit.
PfamiPF01255. Prenyltransf. 1 hit.
[Graphical view]
SUPFAMiSSF64005. SSF64005. 1 hit.
TIGRFAMsiTIGR00055. uppS. 1 hit.
PROSITEiPS01066. UPP_SYNTHASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P9WFF7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARDARKRTS SNFPQLPPAP DDYPTFPDTS TWPVVFPELP AAPYGGPCRP
60 70 80 90 100
PQHTSKAAAP RIPADRLPNH VAIVMDGNGR WATQRGLART EGHKMGEAVV
110 120 130 140 150
IDIACGAIEL GIKWLSLYAF STENWKRSPE EVRFLMGFNR DVVRRRRDTL
160 170 180 190 200
KKLGVRIRWV GSRPRLWRSV INELAVAEEM TKSNDVITIN YCVNYGGRTE
210 220 230 240 250
ITEATREIAR EVAAGRLNPE RITESTIARH LQRPDIPDVD LFLRTSGEQR
260 270 280 290
SSNFMLWQAA YAEYIFQDKL WPDYDRRDLW AACEEYASRT RRFGSA
Length:296
Mass (Da):33,791
Last modified:April 16, 2014 - v1
Checksum:i93895E54253615AA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA. Translation: CCP45149.1.
PIRiH70585.
RefSeqiNP_216877.1. NC_000962.3.
WP_003412212.1. NZ_KK339370.1.

Genome annotation databases

EnsemblBacteriaiCCP45149; CCP45149; Rv2361c.
GeneIDi888964.
KEGGimtu:Rv2361c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA. Translation: CCP45149.1.
PIRiH70585.
RefSeqiNP_216877.1. NC_000962.3.
WP_003412212.1. NZ_KK339370.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2VG2X-ray1.95A/B/C/D13-296[»]
2VG3X-ray1.80A/B/C/D13-296[»]
2VG4X-ray2.60A/B/C/D13-296[»]
4ONCX-ray1.83A/B13-296[»]
ProteinModelPortaliP9WFF7.
SMRiP9WFF7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv2361c.

Proteomic databases

PaxDbiP9WFF7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP45149; CCP45149; Rv2361c.
GeneIDi888964.
KEGGimtu:Rv2361c.

Organism-specific databases

TubercuListiRv2361c.

Phylogenomic databases

eggNOGiENOG4105CR3. Bacteria.
COG0020. LUCA.
KOiK14215.
OMAiWNRPKLE.
PhylomeDBiP9WFF7.

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-6587-MONOMER.

Family and domain databases

CDDicd00475. Cis_IPPS. 1 hit.
Gene3Di3.40.1180.10. 1 hit.
HAMAPiMF_01139. ISPT. 1 hit.
InterProiIPR001441. UPP_synth-like.
IPR018520. UPP_synth-like_CS.
[Graphical view]
PANTHERiPTHR10291. PTHR10291. 1 hit.
PfamiPF01255. Prenyltransf. 1 hit.
[Graphical view]
SUPFAMiSSF64005. SSF64005. 1 hit.
TIGRFAMsiTIGR00055. uppS. 1 hit.
PROSITEiPS01066. UPP_SYNTHASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPDS_MYCTU
AccessioniPrimary (citable) accession number: P9WFF7
Secondary accession number(s): L0T9E4, O05837, P60479
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: November 2, 2016
This is version 17 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.