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2.5.1.96: 4,4'-diapophytoene synthase

This is an abbreviated version!
For detailed information about 4,4'-diapophytoene synthase, go to the full flat file.

Word Map on EC 2.5.1.96

Reaction

2 (2E,6E)-farnesyl diphosphate =

15-cis-4,4'-diapophytoene
+ 2 diphosphate

Synonyms

CrtM, DAP synthase, dehydrosqualene synthase, diapophytoene synthase, DSQ synthase, DSQS

ECTree

     2 Transferases
         2.5 Transferring alkyl or aryl groups, other than methyl groups
             2.5.1 Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)
                2.5.1.96 4,4'-diapophytoene synthase

Crystallization

Crystallization on EC 2.5.1.96 - 4,4'-diapophytoene synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
docking analysis of lapaquistat acetate and squalestatin to crtM. Residues H18, R45, D48, D52, Y129, Q165, N168 and D172 interact with the inhibitors
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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
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
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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