2ICX

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

Summary for 2ICX

• Entry DOI: 10.2210/pdb2icx/pdb
• Related: 1Z90 2ICY
• Descriptor: Probable UTP-glucose-1-phosphate uridylyltransferase 2, DIMETHYL SULFOXIDE, URIDINE 5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: at3g03250, utp, putative udp-glucose pyrophosphorylase, structural genomics functional follow-up study, structural genomics, protein structure initiative, psi, cesg, center for eukaryotic structural genomics, transferase
• Biological source: Arabidopsis thaliana (thale cress)
• Cellular location: Cytoplasm (By similarity): Q9M9P3
• Total number of polymer chains: 2
• Total formula weight: 104554.60

Authors

McCoy, J.G.,Wesenberg, G.E.,Phillips Jr., G.N.,Bitto, E.,Bingman, C.A.,Center for Eukaryotic Structural Genomics (CESG) (deposition date: 2006-09-13, release date: 2006-09-26, Last modification date: 2023-08-30)

Primary citation

McCoy, J.G.,Bitto, E.,Bingman, C.A.,Wesenberg, G.E.,Bannen, R.M.,Kondrashov, D.A.,Phillips Jr., G.N.
Structure and Dynamics of UDP-Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP-Glucose and UTP.
J.Mol.Biol., 366:830-841, 2007

PubMed Abstract: 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.

PubMed: 17178129
DOI: 10.1016/j.jmb.2006.11.059

Experimental method

X-RAY DIFFRACTION (1.85 Å)