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Information on EC 2.5.1.96 - 4,4'-diapophytoene synthase and Organism(s) Staphylococcus aureus and UniProt Accession A9JQL9
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2.5.1.96 4,4'-diapophytoene synthaseIUBMB Comments
Requires Mn2+. Typical of Staphylococcus aureus and some other bacteria such as Heliobacillus sp.
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Word Map
- 2.5.1.96
- staphylococcus
- aureus
-
carotenoid
- staphyloxanthin
-
desaturase
-
head-to-head
- 4,4'-diaponeurosporene
-
allyl
-
carbocation
-
desaturation
-
dimethylallyl
-
head-to-tail
- synthesis
The taxonomic range for the selected organisms is: Staphylococcus aureus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
Synonyms
dehydrosqualene synthase, 4,4'-diapophytoene synthase, diapophytoene synthase, dap synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 (2E,6E)-farnesyl diphosphate = 15-cis-4,4'-diapophytoene + 2 diphosphate
prenyl diphosphate binding site S1 farnesyl diphosphate ionizes to form the 1'-carbocation. This carbocation moves down into the interior of the protein to react with C2,3 in the prenyl diphosphate binding site S2 farnesyl diphosphate. The second PPi then moves up into the S1 site to interact with the three Mg2+, and the cyclopropylcarbinyl cation so formed then rearranges, forming dehydrosqualene binds to the surface pocket
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PATHWAY SOURCE
PATHWAYS
BRENDA
SYSTEMATIC NAME
IUBMB Comments
farnesyl-diphosphate:farnesyl-diphosphate farnesyltransferase (4,4'-diapophytoene forming)
Requires Mn2+. Typical of Staphylococcus aureus and some other bacteria such as Heliobacillus sp.
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
2 (2E,6E)-farnesyl diphosphate
presqualene diphosphate + diphosphate
-
-
-
-
?
presqualene diphosphate
15-cis-4,4'-diapophytoene + diphosphate
-
-
-
-
?
2 (2E,6E)-farnesyl diphosphate
cis-4,4'-diapophytoene + 2 diphosphate
-
-
-
-
?
2 (2E,6E)-farnesyl diphosphate
cis-4,4'-diapophytoene + 2 diphosphate
-
-
-
?
NATURAL SUBSTRATE
NATURAL 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
2 (2E,6E)-farnesyl diphosphate
presqualene diphosphate + diphosphate
-
-
-
-
?
presqualene diphosphate
15-cis-4,4'-diapophytoene + diphosphate
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(3R)-3-biphenyl-4-yl-1-azabicyclo[2.2.2]octan-3-ol
i.e. BPH-651, forms two crystal structures in complex with the enzyme. In both, the quinuclidine headgroup binds in the allylic S1 site with the side chain in S2, but in the presence of diphosphate and Mg2+, the quinuclidine's cationic center interacts with diphosphate and three Mg2+, mimicking a transition state involved in diphosphate ionization
(S)-1-phosphono-4-(3-phenoxyphenyl)butylsulfonic acid
far more active than (R)-compound both in vitro an in cells
1-phosphono-4-[3-(3,4-difluorophenoxy)phenyl]butylsulfonic acid
-
1-phosphono-4-[3-(4-propylphenoxy)phenyl]butylsulfonic acid
potent inhibitor in cell-based assay
2-(4-phenoxyphenoxy)ethyl thiocyanate
i.e. WC-9, binds to the S2 site with its -SCN group surrounded by four hydrogen bond donors
4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid
i.e. BPH-652
4-(4'-butylbiphenyl-4-yl)-1-phosphonobutane-1-sulfonic acid
i.e. BPH-698
4-(biphenyl-4-yl)-1-phosphonobutane-1-sulfonic acid
i.e. BPH-700
N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1-3,7-]dec-2-yl]ethane-1,2-diamine
i.e. SQ-109, forms two crystal structurs in complex with the enzyme. In one, the geranyl side chain binds to either S1 or S2 and the adamantane headgroup binds to S1. In the second, the side chain binds to S2 while the headgroup binds to S1
([[(E)-[[(3E)-4,8-dimethylnona-3,7-dien-1-yl](methyl)iminio]methyl]amino]methyl)(phosphonomethyl)phosphinate
-
competitive inhibitor
lapaquistat acetate
-
docking analysis, interaction with residues H18, R45, D48, D52, Y129, Q165, N168 and D172
squalestatin
-
docking analysis, interaction with residues H18, R45, D48, D52, Y129, Q165, N168 and D172
[([(E)-amino[(4,8-dimethylnonyl)(methyl)iminio]methyl]amino)methyl](phosphonomethyl)phosphinate
-
competitive inhibitor
[[([[(4,8-dimethylnonyl)(methyl)carbamoyl]amino]methyl)(hydroxy)phosphoryl]methyl]phosphonic acid
-
competitive inhibitor
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0000015
4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid
pH not specified in the publication, temperature not specified in the publication
0.000135
4-(4'-butylbiphenyl-4-yl)-1-phosphonobutane-1-sulfonic acid
pH not specified in the publication, temperature not specified in the publication
0.0000002
4-(4-biphenyl)butyldiphosphonic acid
pH not specified in the publication, temperature not specified in the publication
0.000006
4-(biphenyl-4-yl)-1-phosphonobutane-1-sulfonic acid
pH not specified in the publication, temperature not specified in the publication
0.0042
([[(E)-[[(3E)-4,8-dimethylnona-3,7-dien-1-yl](methyl)iminio]methyl]amino]methyl)(phosphonomethyl)phosphinate
-
at pH 7.5 and 37°C
0.0019
[([(E)-amino[(4,8-dimethylnonyl)(methyl)iminio]methyl]amino)methyl](phosphonomethyl)phosphinate
-
at pH 7.5 and 37°C
0.0006
[[([[(4,8-dimethylnonyl)(methyl)carbamoyl]amino]methyl)(hydroxy)phosphoryl]methyl]phosphonic acid
-
at pH 7.5 and 37°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0014
(S)-1-phosphono-4-(3-phenoxyphenyl)butylsulfonic acid
Staphylococcus aureus
pH 7.4, 20°C
0.0022
1-phosphono-4-[3-(3,4-difluorophenoxy)phenyl]butylsulfonic acid
Staphylococcus aureus
pH 7.4, 20°C
0.0021
1-phosphono-4-[3-(3-fluorophenoxy)phenyl]butylsulfonic acid
Staphylococcus aureus
pH 7.4, 20°C
0.0023
1-phosphono-4-[3-(4-fluorophenoxy)phenyl]butylsulfonic acid
Staphylococcus aureus
pH 7.4, 20°C
0.0022
1-phosphono-4-[3-(4-propylphenoxy)phenyl]butylsulfonic acid
Staphylococcus aureus
pH 7.4, 20°C
0.0002
4-[4-(4-trifluoromethylphenyl)phenyl]butyldiphosphonic acid
Staphylococcus aureus
pH 7.4, 20°C
0.045
([[(E)-[[(3E)-4,8-dimethylnona-3,7-dien-1-yl](methyl)iminio]methyl]amino]methyl)(phosphonomethyl)phosphinate
Staphylococcus aureus
-
at pH 7.5 and 37°C
0.017
[([(E)-amino[(4,8-dimethylnonyl)(methyl)iminio]methyl]amino)methyl](phosphonomethyl)phosphinate
Staphylococcus aureus
-
at pH 7.5 and 37°C
0.0055
[[([[(4,8-dimethylnonyl)(methyl)carbamoyl]amino]methyl)(hydroxy)phosphoryl]methyl]phosphonic acid
Staphylococcus aureus
-
at pH 7.5 and 37°C
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
the biosynthesis of 4,4'-diaponeurosporene starts with the condensation of two molecules of farnesyl diphosphate by dehydrosqualene synthase CrtM, the reaction product of this enzyme is dehydrosqualene and not squalene. Dehydrosqualene, i.e.4,4'-diapophytoene, is successively dehydrogenated by desaturase CrtN to form the yellow main intermediate 4,4'-diaponeurosporene
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with three inhibitors bound, to about 2.1 A resolution. with inhibitor (3R)-3-biphenyl-4-yl-1-azabicyclo[2.2.2]octan-3-ol, enzyme forms two crystal structures. In both, the quinuclidine headgroup binds in the allylic S1 site with the side chain in S2, but in the presence of diphosphate and Mg2+, the quinuclidine's cationic center interacts with diphosphate and three Mg2+, mimicking a transition state involved in diphosphate ionization. Inhibitor 2-(4-phenoxyphenoxy)ethyl thiocyanate binds to the S2 site with its -SCN group surrounded by four hydrogen bond donors. Inhibitor N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R,7R)-tricyclo[3.3.1.1-3,7-]dec-2-yl]ethane-1,2-diamine forms two crystal structurs in complex with the enzyme. In one, the geranyl side chain binds to either S1 or S2 and the adamantane headgroup binds to S1. In the second, the side chain binds to S2 while the headgroup binds to S1
in with its reaction intermediate, presqualene diphosphate, the dehydrosqualene product, as well as a series of inhibitors. The results indicate that, on initial diphosphate loss, the primary carbocation so formed bends down into the interior of the protein to react with C2,3 double bond in the prenyl acceptor to form presqualene diphosphate, with the lower two-thirds of both presqualene diphosphate chains occupying essentially the same positions as found in the two farnesyl chains in the substrates. The second-half reaction is then initiated by the presqualene diphosphate returning back to the Mg2+ cluster for ionization, with the resultant dehydrosqualene so formed being trapped in a surface pocket
native protein to 1.58 A resolution. CrtM crystallizes in the P3221 space group and there is one molecule per asymmetric unit. The overall fold shows similarity to that seen in human squalene synthase. In the complex with substrate analogue farnesyl thiodiphosphate, two farnesyl thiodiphosphate molecules are found in the large central cavity. Their diphosphate head groups interact with three Mg2+ ions, which in turn interact with Asp residues in two conserved Asp-X-X-X-Asp repeats. The space group of the complex is P3121, and there are two molecules per asymmetric unit. In docking studies with phosphonosulfonate inhibitors, only one phosphonosulfonate is bound per CrtM. All three inhibitors tested have different binding modes. 4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid binds into the farnesyl thiodiphosphate-1 site with two Mg2+, 4-(4'-butylbiphenyl-4-yl)-1-phosphonobutane-1-sulfonic acid binds into the farnesyl thiodiphosphate-2 site with only one Mg2+, and 4-(biphenyl-4-yl)-1-phosphonobutane-1-sulfonic acid binds into the farnesyl thiodiphosphate-2 site with no Mg2+. The phosphonosulfonate side chains do closely track the locations of the two farnesyl thiodiphosphate inhibitor side chains
docking analysis of lapaquistat acetate and squalestatin to crtM. Residues H18, R45, D48, D52, Y129, Q165, N168 and D172 interact with the inhibitors
-
mutant Y248A in complex with zaragozic acid A, to 2.1 A resolution. Crystals grow in the hexagonal space group P3121 and contain two molecules per asymmetric unit. The active site of each protein is occupied by a molecule zazgozic acid A. The highly oxygenated core structure contacts residues 19SKSF22. The C-1 lipophilic tail extends into the narrow pocket which is lined with hydrophobic residues that help to stabilize the interaction with the isoprenoid moiety of the donor farnesyl diphosphate, S1 site.The side chains of Phe22 and Phe26 are moved toward the bottom of the active site, and the orientation of the Tyr41 side chain provides sufficient space for stabilization of the zaragozic acid A C-1 unit in the S1 site
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Y129A
no activity with substrate farnesyl diphophate, 7% residual activity with geranyl diphosphate
A726G, A850G
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
F26L
-
mutation is sufficient to gain phytoene synthase activity, decrease in dehydrosqualene synthase activity
F26L/E149G
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
F26L/F267S
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
F26L/V43M
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
F26S/I40T
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
H12R/F26L/D27G/90G/K97R/H207R
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
K20E/F26S
-
mutant with phytoene synthase activity, decrease in dehydrosqualene synthase activity
M4V/H12R/F59S/Q81R/E180G
-
mutant with phytoene synthase activity, without decrease in dehydrosqualene synthase activity
additional information
-
construction of C40 carotenoid synthase pathway in Escherichia coli by expression of crtE encoding GGPP synthase, crtB encoding phytoene synthase, and crtI encoding phytoene desaturase, all from Erwinia uredovora. Replacement of phytoene synthase crtB by dehydrosqualene synthase crtM results in negligible ability to synthesize the C40 product. Some crtM mutants perform comparably to crtB in an in vivo C40 pathway. These mutants show significant variation in performance in their original C30 pathway, indicating the emergence of enzymes with broadened substrate specificity as well as those with shifted specificity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
-
construction of an in vitro C30 carotenoid pathway based on recombinant Escherichia coli farnesyl diphosphate synthase and 4,4'-diapophytoene synthase. The 4,4'-diapophytoene product is unstabel in aqueous buffer. In situ extraction using an aqueous-organic two-phase system results in a 100% conversion of isopentenyl diphosphate and dimethylallyl diphosphate into 4,4'-diapophytoene synthase
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ku, B.; Jeong, J.C.; Mijts, B.N.; Schmidt-Dannert, C.; Dordick, J.S.
Preparation, characterization, and optimization of an in vitro C30 carotenoid pathway
Appl. Environ. Microbiol.
71
6578-6583
2005
Staphylococcus aureus
Wieland, B.; Feil, C.; Gloria-Maercker, E.; Thumm, G.; Lechner, M.; Bravo, J.M.; Poralla, K.; Gotz, F.
Genetic and biochemical analyses of the biosynthesis of the yellow carotenoid 4,4'-diaponeurosporene of Staphylococcus aureus
J. Bacteriol.
176
7719-7726
1994
Staphylococcus aureus (O07854), Staphylococcus aureus, Staphylococcus aureus Newman (O07854), Staphylococcus aureus Newman
Umeno, D.; Arnold, F.
Evolution of a pathway to novel long-chain carotenoids
J. Bacteriol.
186
1531-1536
2004
Staphylococcus aureus, Staphylococcus aureus ATCC 35556
Kahlon, A.; Roy, S.; Sharma, A.
Molecular docking studies to map the binding site of squalene synthase inhibitors on dehydrosqualene synthase of Staphylococcus aureus
J. Biomol. Struct. Dyn.
28
201-210
2010
Staphylococcus aureus
Song, Y.; Lin, F.; Yin, F.; Hensler, M.; Poveda, C.; Mukkamala, D.; Cao, R.; Wang, H.; Morita, C.; Pacanowska, D.; Nizet, V.; Oldfield, E.
Phosphonosulfonates are potent, selective inhibitors of dehydrosqualene synthase and staphyloxanthin biosynthesis in Staphylococcus aureus
J. Med. Chem.
52
976-988
2009
Staphylococcus aureus (A9JQL9), Staphylococcus aureus
Lin, F.; Liu, C.; Liu, Y.; Zhang, Y.; Wang, K.; Jeng, W.; Ko, T.; Cao, R.; Wang, A.; Oldfield, E.
Mechanism of action and inhibition of dehydrosqualene synthase
Proc. Natl. Acad. Sci. USA
107
21337-21342
2010
Staphylococcus aureus (A9JQL9), Staphylococcus aureus
Liu, C.; Liu, G.; Song, Y.; Yin, F.; Hensler, M.; Jeng, W.; Nizet, V.; Wang, A.; Oldfield, E.
A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence
Science
319
1391-1394
2008
Staphylococcus aureus (A9JQL9), Staphylococcus aureus
Liu, C.I.; Jeng, W.Y.; Chang, W.J.; Ko, T.P.; Wang, A.H.
Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase
J. Biol. Chem.
287
18750-18757
2012
Staphylococcus aureus
Lin, F.Y.; Liu, Y.L.; Li, K.; Cao, R.; Zhu, W.; Axelson, J.; Pang, R.; Oldfield, E.
Head-to-head prenyl tranferases: anti-infective drug targets
J. Med. Chem.
55
4367-4372
2012
Staphylococcus aureus (A9JQL9), Staphylococcus aureus
Abdelmagid, W.M.; Adak, T.; Freeman, J.O.; Tanner, M.E.
Studies with guanidinium- and amidinium-based inhibitors suggest minimal stabilization of allylic carbocation intermediates by dehydrosqualene and squalene synthases
Biochemistry
57
5591-5601
2018
Staphylococcus aureus, Staphylococcus aureus MS4
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