BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//CERN//INDICO//EN
BEGIN:VEVENT
SUMMARY:In crystallo study of the reaction mechanism in a family B DNA pol
 ymerase
DTSTART;VALUE=DATE-TIME:20250922T153000Z
DTEND;VALUE=DATE-TIME:20250922T154000Z
DTSTAMP;VALUE=DATE-TIME:20260525T195544Z
UID:indico-contribution-1835@lindico453.srv.lu.se
DESCRIPTION:Speakers: Vimal Parkash (Umeå University)\nReaction intermedi
 ates during DNA synthesis have been studied in detail using time-resolved\
 nX-ray crystallography for translesion and repair DNA polymerases. Contrar
 y to the originally\nproposed two-metal-ion mechanism\, a third metal ion 
 was identified between the finger\ndomain and the α- and β-phosphates of
  the incoming nucleotide. This third metal ion was\nsuggested to either pa
 rticipate in catalysis or stabilize product formation. To investigate this
 \nfurther in a replicative polymerase\, we conducted time-resolved X-ray c
 rystallography with\nDNA Polymerase epsilon\, which synthesizes DNA at a m
 uch faster rate—10x to 100x higher\nthan family Y and X polymerases. Sur
 prisingly\, no metal ion was observed between the finger\ndomain and the 
 α- and β-phosphates of the incoming nucleotide in any of the solved stru
 ctures\nwith Pol epsilon. Instead\, our biochemical and structural data su
 pport the original two-metal\nmechanism. In addition\, we discovered that 
 the 3’-OH group releases a proton\, which is\nchanneled via structural w
 aters to a basic residue in the Palm domain. After forming a new\nbond wit
 h the incoming nucleotide\, an acidic residue in the finger domain protona
 tes the\nreleased pyrophosphate\, stabilizing the product. In summary\, it
  seems that metal A’s role is\nto lower the pKa of the 3’-OH group\, f
 ollowed by specific residues in Pol epsilon donating or\nreceiving a proto
 n to catalyze this acid-base reaction.\n\nCo-author: Erik Johansson\n\nhtt
 ps://lindico453.srv.lu.se/event/583/contributions/1835/
LOCATION:LINXS at The Loop
URL:https://lindico453.srv.lu.se/event/583/contributions/1835/
END:VEVENT
END:VCALENDAR