1x08: Difference between revisions

Revision as of 16:49, 21 February 2008

Crystal structure of D26A mutant UPPs in complex with Mg, IPP and FsPP

OverviewOverview

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.

About this StructureAbout this Structure

1X08 is a Single protein structure of sequence from Escherichia coli with and as ligands. Active as Di-trans,poly-cis-decaprenylcistransferase, with EC number 2.5.1.31 Full crystallographic information is available from OCA.

ReferenceReference

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., Guo RT, Ko TP, Chen AP, Kuo CJ, Wang AH, Liang PH, J Biol Chem. 2005 May 27;280(21):20762-74. Epub 2005 Mar 23. PMID:15788389

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-[[Image:1x08.gif|left|200px]]<br /><applet load="1x08" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1x08.gif|left|200px]]<br /><applet load="1x08" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1x08, resolution 1.9&Aring;" />
 '''Crystal structure of D26A mutant UPPs in complex with Mg, IPP and FsPP'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-X08 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with FPS and IPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Di-trans,poly-cis-decaprenylcistransferase Di-trans,poly-cis-decaprenylcistransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1X08 OCA].
+X08 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=FPS:'>FPS</scene> and <scene name='pdbligand=IPE:'>IPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Di-trans,poly-cis-decaprenylcistransferase Di-trans,poly-cis-decaprenylcistransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X08 OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
-[[Category: Chen, A.P.C.]]
+[[Category: Chen, A P.C.]]
-[[Category: Guo, R.T.]]
+[[Category: Guo, R T.]]
-[[Category: Ko, T.P.]]
+[[Category: Ko, T P.]]
-[[Category: Kuo, C.J.]]
+[[Category: Kuo, C J.]]
-[[Category: Liang, P.H.]]
+[[Category: Liang, P H.]]
-[[Category: Wang, A.H.J.]]
+[[Category: Wang, A H.J.]]
 [[Category: FPS]]
 [[Category: IPE]]
 [[Category: inactive mutant enzyme-substrate complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:46:24 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:49:50 2008''