skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly

Journal Article · · BMC Structural Biology (Online)
 [1];  [1];  [1];  [2];  [1];  [3]
  1. Univ. of Alabama, Birmingham, AL (United States). Center for Biophysical Sciences and Engineering
  2. BioCryst Pharmaceuticals, Birmingham, AL (United States)
  3. Univ. of Alabama, Birmingham, AL (United States). Center for Biophysical Sciences and Engineering; Univ. of Alabama, Birmingham, AL (United States). Dept. of Medicine
+ Show Author Affiliations

Background: Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms in primary, secondary and tertiary structure and characteristic motifs. It adopted a novel catalysis-independent role in DNA replication that involves interaction with a viral protein, A20, to form the processivity factor. UDG:A20 association is essential for assembling of the processive DNA polymerase complex. The structure of the protein must have provisions for such interactions with A20. This paper provides the first glimpse into the structure of a poxvirus UDG. Results: Results of dynamic light scattering experiments and native size exclusion chromatography showed that vvUDG is a dimer in solution. The dimeric assembly is also maintained in two crystal forms. The core of vvUDG is reasonably well conserved but the structure contains one additional β-sheet at each terminus. A glycerol molecule is found in the active site of the enzyme in both crystal forms. Interaction of this glycerol molecule with the protein possibly mimics the enzyme substrate (uracil) interactions. Conclusion: The crystal structures reveal several distinctive features of vvUDG. The new structural features may have evolved for adopting novel functions in the replication machinery of poxviruses. The mode of interaction between the subunits in the dimers suggests a possible model for binding to its partner and the nature of the processivity factor in the polymerase complex.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH)
Grant/Contract Number:
AC02-06CH11357; U54 AI 057157; W-31-109-ENG-38
OSTI ID:
1626553
Journal Information:
BMC Structural Biology (Online), Vol. 7, Issue 1; ISSN 1472-6807
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (34)

Characterisation of the substrate specificity of homogeneous vaccinia virus uracil-DNA glycosylase journal August 2003
Vaccinia Virus Uracil DNA Glycosylase Interacts with the A20 Protein to Form a Heterodimeric Processivity Factor for the Viral DNA Polymerase journal December 2005
Mutations in active-site residues of the uracil-DNA glycosylase encoded by vaccinia virus are incompatible with virus viability journal November 1996
Vaccinia Virus Uracil DNA Glycosylase Has an Essential Role in DNA Synthesis That Is Independent of Its Glycosylase Activity: Catalytic Site Mutations Reduce Virulence but Not Virus Replication in Cultured Cells journal January 2003
Mapping Interaction Sites of the A20R Protein Component of the Vaccinia Virus DNA Replication Complex journal November 2002
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces journal June 2006
Crystal structure ofEscherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: Structure and glycosylase mechanism revisited journal April 1999
Role of Electrophilic and General Base Catalysis in the Mechanism of Escherichia coli Uracil DNA Glycosylase † journal September 1999
Kinetic Mechanism of Damage Site Recognition and Uracil Flipping by Escherichia coli Uracil DNA Glycosylase † journal January 1999
Reconstructing the Substrate for Uracil DNA Glycosylase:  Tracking the Transmission of Binding Energy in Catalysis journal May 2001
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA journal September 1998
Envisioning the molecular choreography of DNA base excision repair journal February 1999
Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects journal May 2000
Stressing-Out DNA? The Contribution of Serine−Phosphodiester Interactions in Catalysis by Uracil DNA Glycosylase † journal October 2000
Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase 1 1Edited by D. C. Rees journal March 1999
X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG journal November 1998
The structural basis of specific base-excision repair by uracil–DNA glycosylase journal February 1995
Lessons learned from structural results on uracil-DNA glycosylase journal August 2000
Crystal structure and mutational analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis journal March 1995
Building a Replisome from Interacting Pieces journal October 1999
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
The finer things in X-ray diffraction data collection journal October 1999
Substructure solution with SHELXD journal September 2002
Macromolecular phasing with SHELXE journal January 2002
MOLREP an Automated Program for Molecular Replacement journal December 1997
PHENIX : building new software for automated crystallographic structure determination journal October 2002
Coot model-building tools for molecular graphics journal November 2004
Recent developments for the efficient crystallographic refinement of macromolecular structures journal October 1998
Refinement of Macromolecular Structures by the Maximum-Likelihood Method journal May 1997
GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences book January 2003
PDBsum: summaries and analyses of PDB structures journal January 2001
The Role of Leucine 191 of Escherichia coliUracil DNA Glycosylase in the Formation of a Highly Stable Complex with the Substrate Mimic, Ugi, and in Uracil Excision from the Synthetic Substrates journal May 2001
Flexibility revealed by the 1.85 Å crystal structure of the β sliding-clamp subunit of Escherichia coli DNA polymerase III journal June 2003
Structure of the heterotrimeric PCNA from Sulfolobus solfataricus journal September 2006

Cited By (7)

Uracil-DNA glycosylases-Structural and functional perspectives on an essential family of DNA repair enzymes: Uracil-DNA Glycosylases journal October 2014
Architecturally diverse proteins converge on an analogous mechanism to inactivate Uracil-DNA glycosylase journal July 2013
Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity journal March 2017
Effects of vaccinia virus uracil DNA glycosylase catalytic site and deoxyuridine triphosphatase deletion mutations individually and together on replication in active and quiescent cells and pathogenesis in mice journal January 2008
Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase journal June 2015
Crystal structure of mimivirus uracil-DNA glycosylase journal August 2017
Crystal Structure of the Vaccinia Virus DNA Polymerase Holoenzyme Subunit D4 in Complex with the A20 N-Terminal Domain journal March 2014

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biophysics