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Information on EC 2.5.1.31 - ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] and Organism(s) Helicobacter pylori and UniProt Accession P55984
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2.5.1.31 ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]IUBMB Comments
Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall .
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Word Map
- 2.5.1.31
-
isoprenoids
- cis-prenyltransferase
- prenyltransferases
- dolichols
- luteus
- dhdds
- trans-prenyltransferases
- pharmacology
-
octaprenyl
- drug development
- medicine
The taxonomic range for the selected organisms is: Helicobacter pylori
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
Synonyms
undecaprenyl diphosphate synthase, undecaprenyl pyrophosphate synthase, dehydrodolichyl diphosphate synthase, upp synthase, ddpps, undecaprenyl pyrophosphate synthetase, upp synthetase, z-prenyl diphosphate synthase, isosesquilavandulyl diphosphate synthase, undecaprenyl-diphosphate synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
bactoprenyl-diphosphate synthase
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C55-OO synthetase
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-
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C55PP synthetase
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-
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cis,polyprenyl diphosphate synthase
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-
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CPDS
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DDPPs
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dehydrodolichyl diphosphate synthase
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di-trans,poly-cis-undecaprenyl-diphosphate synthase
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synthetase, undecaprenyl pyrophosphate
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undecaprenyl diphosphate synthase
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undecaprenyl diphosphate synthetase
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undecaprenyl pyrophosphate synthetase
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undecaprenyl-diphosphate synthase
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UPP synthetase
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UPS
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Z-prenyl diphosphate synthase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
alkenyl group transfer
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
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SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 8 isopentenyl units)
Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall [3].
CAS REGISTRY NUMBER
COMMENTARY
52350-87-5
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate
8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
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-
-
?
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + ditrans,polycis-undecaprenyl diphosphate
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-
-
?
farnesyl diphosphate + isopentenyl diphosphate
diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
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-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
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3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
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3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
i.e. HTS04781, crystallization data. The sulfonamide group forms H-bonds with Gly16 and Arg26 and the N atom in the tetracyclic ring is hydrogen bound to the main chain of Met12. Extensive hydrophobic interactions are found between the tetracyclic ring with the surrounding residues including Met12, His30, Gly33 and Val34
N,N'-bis(6-chloro-1,3-benzothiazol-2-yl)methanedisulfonamide
i.e. BTB06061, crystallization data. The sulfur atom in the thiazole ring of BTB06061 may form H-bonds with Asn15 and His30 while the SO2 group is hydrogen bound with Met12. The aromatic rings of BTB06061 form hydrophobic interactions with the surrounding hydrophobic residues, including Val34, Leu37, Ala56 and Tyr79
additional information
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virtual screening of inhibitors from a library of 58635 compounds performed
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additional information
virtual screening of inhibitors from a library of 58635 compounds performed
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00011
(2E,6E)-farnesyl diphosphate
wild type, pH 7.5, temperature not specified in the publication
0.00015
(2E,6E)-farnesyl diphosphate
mutant C234A, pH 7.5, temperature not specified in the publication
0.0092
(2E,6E)-farnesyl diphosphate
wild type, pH 7.5, temperature not specified in the publication
0.0096
(2E,6E)-farnesyl diphosphate
mutant C234A, pH 7.5, temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.2
(2E,6E)-farnesyl diphosphate
mutant C234A, pH 7.5, temperature not specified in the publication
0.22
(2E,6E)-farnesyl diphosphate
wild type, pH 7.5, temperature not specified in the publication
0.2
(2E,6E)-farnesyl diphosphate
mutant C234A, co-substrate: isopentenyl diphosphate
0.22
(2E,6E)-farnesyl diphosphate
wild-type, co-substrate: isopentenyl diphosphate
0.2
isopentenyl diphosphate
mutant C234A, co-substrate: farnesyl diphosphate
0.22
isopentenyl diphosphate
wild-type, co-substrate: farnesyl diphosphate
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.362
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
Helicobacter pylori
pH 7.5, temperature not specified in the publication
0.35
N,N'-bis(6-chloro-1,3-benzothiazol-2-yl)methanedisulfonamide
Helicobacter pylori
pH 7.5, temperature not specified in the publication
0.362
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
0.362
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
Helicobacter pylori
pH 7.5
0.362
3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide
Helicobacter pylori
IC50 value of this compound is equal against the C234A mutant and wild-type
0.35
N,N'-bis(6-chloro-1,3-benzothiazol-2-yl)methanedisulfonamide
Helicobacter pylori
pH 7.5
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
each subunit contains a catalytic domain and a pairing domain
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of Helicobacter pylori UPPS and mutant by hanging drop method
C234A UPPS mutant to prevent intra-molecular disulfide bond formed during the long period of crystallization process is crystallized using the hanging drop method. The protein is a dimer and each subunit contains a catalytic domain and a pairing domain. Two subunits are tightly associated through the central beta-sheet and a pair of long alpha-helices. Helicobacter pylori UPPS has a 1.5-turn shorter alpha5 helix in the dimer interface. This may weaken the dimer formation for Helicobacter pylori UPPS. The catalytic domain is composed of six beta-strands and four beta-helices and the central tunnel-shaped active site is surrounded by 2 alpha-helices and 4 beta-strands
in complex with farnesyl diphosphate. Virtual screening of inhibitors from a library of 58,635 compounds, modelling of inhibitors N,N'-bis(6-chloro-1,3-benzothiazol-2-yl)methanedisulfonamide and 3-[5-(5,6-dihydrobenzimidazo[1,2-c]quinazolin-6-yl)-2,5-dihydrofuran-2-yl]benzenesulfonamide into structure
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C234A
site-directed mutagenesis, mutation to prevent intramolecular disulfide bond formed during the long period of crystallization process
C234A
C234A
C234A UPPS mutant is crystallized using the hanging drop method, C234A has unchanged kinetic properties compared to wild-type
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
enzyme represents a potential target for developing new antibiotics
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kuo, C.; Guo, R.; Lu, I.; Liu, H.; Wu, S.; Ko, T.; Wang, A.H.; Liang, P.
Structure-based inhibitors exhibit differential activities against Helicobacter pylori and Escherichia coli undecaprenyl pyrophosphate synthases
J. Biomed. Biotechnol.
2008
841312
2008
Escherichia coli, Escherichia coli (P60472), Helicobacter pylori, Helicobacter pylori (P55984)
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