2icx: Difference between revisions

Revision as of 07:20, 4 May 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. 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 Sun May 4 07:20:47 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:2icx.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2icx |SIZE=350|CAPTION= <scene name='initialview01'>2icx</scene>, resolution 1.850&Aring;
+The line below this paragraph, containing "STRUCTURE_2icx", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=UTP:URIDINE+5&#39;-TRIPHOSPHATE'>UTP</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= At3g03250, T17B22.6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
+-->
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01704 UDPGP]</span>
+{{STRUCTURE_2icx|  PDB=2icx  |  SCENE=  }}
-|RELATEDENTRY=[[1z90|1Z90]], [[2icy|2ICY]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2icx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2icx OCA], [http://www.ebi.ac.uk/pdbsum/2icx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2icx RCSB]</span>
-}}
 '''Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP'''
@@ Line 32: / Line 29: @@
 [[Category: McCoy, J G.]]
 [[Category: Wesenberg, G E.]]
-[[Category: at3g03250]]
+[[Category: At3g03250]]
-[[Category: center for eukaryotic structural genomic]]
+[[Category: Center for eukaryotic structural genomic]]
-[[Category: cesg]]
+[[Category: Cesg]]
-[[Category: protein structure initiative]]
+[[Category: Protein structure initiative]]
-[[Category: psi]]
+[[Category: Psi]]
-[[Category: putative udp-glucose pyrophosphorylase]]
+[[Category: Putative udp-glucose pyrophosphorylase]]
-[[Category: structural genomic]]
+[[Category: Structural genomic]]
-[[Category: structural genomics functional follow-up study]]
+[[Category: Structural genomics functional follow-up study]]
-[[Category: utp]]
+[[Category: Utp]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:20:47 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:42:39 2008''