PMID- 17098747
OWN - NLM
STAT- MEDLINE
DA  - 20070108
DCOM- 20070307
LR  - 20161122
IS  - 0021-9258 (Print)
IS  - 0021-9258 (Linking)
VI  - 282
IP  - 2
DP  - 2007 Jan 12
TI  - Structural and biochemical investigation of the role in proofreading of a beta
      hairpin loop found in the exonuclease domain of a replicative DNA polymerase of
      the B family.
PG  - 1432-44
AB  - Replicative DNA polymerases, as exemplified by the B family polymerases from
      bacteriophages T4 and RB69, not only replicate DNA but also have the ability to
      proofread misincorporated nucleotides. Because the two activities reside in
      separate protein domains, polymerases must employ a mechanism that allows for
      efficient switching of the primer strand between the two active sites to achieve 
      fast and accurate replication. Prior mutational and structural studies suggested 
      that a beta hairpin structure located in the exonuclease domain of family B
      polymerases might play an important role in active site switching in the event of
      a nucleotide misincorporation. We show that deleting the beta hairpin loop in
      RB69 gp43 affects neither polymerase nor exonuclease activities. Single binding
      event studies with mismatched primer termini, however, show that the beta hairpin
      plays a role in maintaining the stability of the polymerase/DNA interactions
      during the binding of the primer DNA in the exonuclease active site but not on
      the return of the corrected primer to the polymerase active site. In addition,
      the deletion variant showed a more stable incorporation of a nucleotide opposite 
      an abasic site. Moreover, in the 2.4 A crystal structure of the beta hairpin
      deletion variant incorporating an A opposite a templating furan, all four
      molecules in the crystal asymmetric unit have DNA in the polymerase active site, 
      despite the presence of DNA distortions because of the misincorporation,
      confirming that the primer strand is not stably bound within the exonuclease
      active site in the absence of the beta hairpin loop.
FAU - Hogg, Matthew
AU  - Hogg M
AD  - Department of Microbiology and Molecular Genetics, University of Vermont,
      Burlington, Vermont 05405, USA.
FAU - Aller, Pierre
AU  - Aller P
FAU - Konigsberg, William
AU  - Konigsberg W
FAU - Wallace, Susan S
AU  - Wallace SS
FAU - Doublie, Sylvie
AU  - Doublie S
LA  - eng
SI  - PDB/2DTU
GR  - R01 CA052040-16/CA/NCI NIH HHS/United States
GR  - CA52040/CA/NCI NIH HHS/United States
GR  - Y1-GM-1104/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20061109
PL  - United States
TA  - J Biol Chem
JT  - The Journal of biological chemistry
JID - 2985121R
RN  - 0 (DNA, Single-Stranded)
RN  - 0 (Viral Proteins)
RN  - 0 (gene 43 protein, Enterobacteria phage T4)
RN  - EC 2.7.7.7 (DNA-Directed DNA Polymerase)
RN  - EC 2.7.7.7 (bacteriophage RB69 DNA polymerase)
RN  - EC 3.1.- (Exodeoxyribonucleases)
SB  - IM
MH  - Bacteriophage T4/*enzymology/genetics
MH  - Binding Sites/genetics
MH  - Crystallography
MH  - *DNA Replication
MH  - DNA, Single-Stranded/genetics/metabolism
MH  - DNA-Directed DNA Polymerase/*chemistry/metabolism
MH  - Enzyme Activation
MH  - Exodeoxyribonucleases/*chemistry/metabolism
MH  - Gene Deletion
MH  - Protein Structure, Quaternary
MH  - Protein Structure, Tertiary
MH  - Viral Proteins/*chemistry/metabolism
EDAT- 2006/11/14 09:00
MHDA- 2007/03/08 09:00
CRDT- 2006/11/14 09:00
AID - M605675200 [pii]
AID - 10.1074/jbc.M605675200 [doi]
PST - ppublish
SO  - J Biol Chem. 2007 Jan 12;282(2):1432-44. Epub 2006 Nov 9.