2icx: Difference between revisions

Revision as of 18:51, 21 February 2008

Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP

OverviewOverview

The structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 Angstroms. In addition, the structure has been solved in the presence of the substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 Angstroms and 1.85 Angstroms. The three structures revealed a catalytic domain similar to that of other nucleotidyl-glucose pyrophosphorylases with a carboxy-terminal beta-helix domain in a unique orientation. Conformational changes are observed between the native and substrate-bound complexes. The nucleotide-binding loop and the carboxy-terminal domain, including the suspected catalytically important Lys360, move in and out of the active site in a concerted fashion. TLS refinement was employed initially to model conformational heterogeneity in the UDP-glucose complex followed by the use of multiconformer refinement for the entire molecule. Normal mode analysis generated atomic displacement predictions in good agreement in magnitude and direction with the observed conformational changes and anisotropic displacement parameters generated by TLS refinement. The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity.

About this StructureAbout this Structure

2ICX is a Single protein structure of sequence from Arabidopsis thaliana with and as ligands. Active as UTP--glucose-1-phosphate uridylyltransferase, with EC number 2.7.7.9 Full crystallographic information is available from OCA.

ReferenceReference

Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP., McCoy JG, Bitto E, Bingman CA, Wesenberg GE, Bannen RM, Kondrashov DA, Phillips GN Jr, J Mol Biol. 2007 Feb 23;366(3):830-41. Epub 2006 Nov 21. PMID:17178129

Page seeded by OCA on Thu Feb 21 17:51:22 2008

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OCA

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-[[Image:2icx.gif|left|200px]]<br /><applet load="2icx" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2icx.gif|left|200px]]<br /><applet load="2icx" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2icx, resolution 1.850&Aring;" />
 '''Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP'''<br />
 ==Overview==
-The structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis, thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 A., In addition, the structure has been solved in the presence of the, substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 A, and 1.85 A. The three structures revealed a catalytic domain similar to, that of other nucleotidyl-glucose pyrophosphorylases with a, carboxy-terminal beta-helix domain in a unique orientation. Conformational, changes are observed between the native and substrate-bound complexes. The, nucleotide-binding loop and the carboxy-terminal domain, including the, suspected catalytically important Lys360, move in and out of the active, site in a concerted fashion. TLS refinement was employed initially to, model conformational heterogeneity in the UDP-glucose complex followed by, the use of multiconformer refinement for the entire molecule. Normal mode, analysis generated atomic displacement predictions in good agreement in, magnitude and direction with the observed conformational changes and, anisotropic displacement parameters generated by TLS refinement. The, structures and the observed dynamic changes provide insight into the, ordered mechanism of this enzyme and previously described oligomerization, effects on catalytic activity.
+The structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 Angstroms. In addition, the structure has been solved in the presence of the substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 Angstroms and 1.85 Angstroms. The three structures revealed a catalytic domain similar to that of other nucleotidyl-glucose pyrophosphorylases with a carboxy-terminal beta-helix domain in a unique orientation. Conformational changes are observed between the native and substrate-bound complexes. The nucleotide-binding loop and the carboxy-terminal domain, including the suspected catalytically important Lys360, move in and out of the active site in a concerted fashion. TLS refinement was employed initially to model conformational heterogeneity in the UDP-glucose complex followed by the use of multiconformer refinement for the entire molecule. Normal mode analysis generated atomic displacement predictions in good agreement in magnitude and direction with the observed conformational changes and anisotropic displacement parameters generated by TLS refinement. The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity.
 ==About this Structure==
-ICX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with DMS and UTP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2ICX OCA].
+ICX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=DMS:'>DMS</scene> and <scene name='pdbligand=UTP:'>UTP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ICX OCA].
 ==Reference==
-Structure and Dynamics of UDP-Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP-Glucose and UTP., McCoy JG, Bitto E, Bingman CA, Wesenberg GE, Bannen RM, Kondrashov DA, Phillips GN Jr, J Mol Biol. 2007 Feb 23;366(3):830-41. Epub 2006 Nov 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17178129 17178129]
+Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP., McCoy JG, Bitto E, Bingman CA, Wesenberg GE, Bannen RM, Kondrashov DA, Phillips GN Jr, J Mol Biol. 2007 Feb 23;366(3):830-41. Epub 2006 Nov 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17178129 17178129]
 [[Category: Arabidopsis thaliana]]
 [[Category: Single protein]]
 [[Category: UTP--glucose-1-phosphate uridylyltransferase]]
-[[Category: Bingman, C.A.]]
+[[Category: Bingman, C A.]]
 [[Category: Bitto, E.]]
-[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
+[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
-[[Category: Jr., G.N.Phillips.]]
+[[Category: Jr., G N.Phillips.]]
-[[Category: McCoy, J.G.]]
+[[Category: McCoy, J G.]]
-[[Category: Wesenberg, G.E.]]
+[[Category: Wesenberg, G E.]]
 [[Category: DMS]]
 [[Category: UTP]]
@@ Line 32: / Line 32: @@
 [[Category: utp]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:15:05 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:51:22 2008''