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Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP.

TitleStructure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP.
Publication TypeJournal Article
Year of Publication2007
AuthorsMcCoy JG, Bitto E, Bingman CA, Wesenberg GE, Bannen RM, Kondrashov DA, Phillips GN
JournalJ Mol Biol
Volume366
Issue3
Pagination830-41
Date Published2007 Feb 23
ISSN0022-2836
KeywordsArabidopsis, Binding Sites, Humans, Models, Molecular, Protein Folding, Protein Structure, Quaternary, Protein Structure, Secondary, Structure-Activity Relationship, Substrate Specificity, Uridine Diphosphate Glucose, Uridine Triphosphate, UTP-Glucose-1-Phosphate Uridylyltransferase
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.

DOI10.1016/j.jmb.2006.11.059
Alternate JournalJ. Mol. Biol.
PubMed ID17178129
PubMed Central IDPMC1847403
Grant ListP50 GM064598-04 / GM / NIGMS NIH HHS / United States
P50 GM64598 / GM / NIGMS NIH HHS / United States
T15 LM007359 / LM / NLM NIH HHS / United States
T15 LM007359 / LM / NLM NIH HHS / United States
T15 LM007359-05 / LM / NLM NIH HHS / United States
U54 GM074901 / GM / NIGMS NIH HHS / United States
U54 GM074901-01 / GM / NIGMS NIH HHS / United States