1X09

Crystal structure of the D26A mutant UPPs in complex with magnesium and isopentenyl pyrophosphate

Summary for 1X09

• Entry DOI: 10.2210/pdb1x09/pdb
• Related: 1JP3 1UEH 1V7U 1X06 1X07 1X08
• Descriptor: Undecaprenyl pyrophosphate synthetase, MAGNESIUM ION, 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: enzyme substrate complex, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 28953.61

Authors

Guo, R.-T.,Ko, T.-P.,Chen, A.P.-C.,Kuo, C.-J.,Wang, A.H.-J.,Liang, P.-H. (deposition date: 2005-03-15, release date: 2005-03-22, Last modification date: 2023-10-25)

Primary citation

Guo, R.T.,Ko, T.P.,Chen, A.P.,Kuo, C.J.,Wang, A.H.,Liang, P.H.
Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis.
J.Biol.Chem., 280:20762-20774, 2005

PubMed Abstract: Undecaprenyl pyrophosphate synthase (UPPs) catalyzes the consecutive condensation reactions of a farnesyl pyrophosphate (FPP) with eight isopentenyl pyrophosphates (IPP), in which new cis-double bonds are formed, to generate undecaprenyl pyrophosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall. The structures of Escherichia coli UPPs were determined previously in an orthorhombic crystal form as an apoenzyme, in complex with Mg(2+)/sulfate/Triton, and with bound FPP. In a further search of its catalytic mechanism, the wild-type UPPs and the D26A mutant are crystallized in a new trigonal unit cell with Mg(2+)/IPP/farnesyl thiopyrophosphate (an FPP analogue) bound to the active site. In the wild-type enzyme, Mg(2+) is coordinated by the pyrophosphate of farnesyl thiopyrophosphate, the carboxylate of Asp(26), and three water molecules. In the mutant enzyme, it is bound to the pyrophosphate of IPP. The [Mg(2+)] dependence of the catalytic rate by UPPs shows that the activity is maximal at [Mg(2+)] = 1 mm but drops significantly when Mg(2+) ions are in excess (50 mm). Without Mg(2+), IPP binds to UPPs only at high concentration. Mutation of Asp(26) to other charged amino acids results in significant decrease of the UPPs activity. The role of Asp(26) is probably to assist the migration of Mg(2+) from IPP to FPP and thus initiate the condensation reaction by ionization of the pyrophosphate group from FPP. Other conserved residues, including His(43), Ser(71), Asn(74), and Arg(77), may serve as general acid/base and pyrophosphate carrier. Our results here improve the understanding of the UPPs enzyme reaction significantly.

PubMed: 15788389
DOI: 10.1074/jbc.M502121200

Experimental method

X-RAY DIFFRACTION (1.87 Å)