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A double role for a strictly conserved serine: Further insights into the dUTPase catalytic mechanism

Palmen, Lorena Gonzalez; Becker, Kristian LU ; Bülow, Leif LU and Kvassman, Jan-Olov (2008) In Biochemistry 47(30). p.7863-7874
Abstract
Ser72 at the active site of the Escherichia coli dUTPase has been mutated to an alanine, and the properties of the mutant have been investigated. The serine is absolutely conserved among the monomeric and trimeric dUTPases (including the bifunctional dCTP deaminase:dUTPases), and it has been proposed to promote catalysis by balancing negative charge at the oxygen that bridges the alpha- and beta-pbosphorus of the substrate. In all reported complexes of dUTPases with the substrate analogue alpha,beta-imido-dUTP center dot Mg, the serine beta-OH is indeed hydrogen bonded to the alpha,beta-bridging nitrogen of the analogue. However, in the complex of the Asp90 -> Asn mutant dUTPase with the true substrate dUTP center dot Mg, the serine... (More)
Ser72 at the active site of the Escherichia coli dUTPase has been mutated to an alanine, and the properties of the mutant have been investigated. The serine is absolutely conserved among the monomeric and trimeric dUTPases (including the bifunctional dCTP deaminase:dUTPases), and it has been proposed to promote catalysis by balancing negative charge at the oxygen that bridges the alpha- and beta-pbosphorus of the substrate. In all reported complexes of dUTPases with the substrate analogue alpha,beta-imido-dUTP center dot Mg, the serine beta-OH is indeed hydrogen bonded to the alpha,beta-bridging nitrogen of the analogue. However, in the complex of the Asp90 -> Asn mutant dUTPase with the true substrate dUTP center dot Mg, the serine P-OH points in the opposite direction and may form a hydrogen bond to Asn84 at the bottom of the pyrimidine pocket. Here we show that the replacement of the P-OH by hydrogen reduces k(cat) from 5.8 to 0.008 s(-1) but also k(-1), the rate of substrate dissociation, from 6.2 to 0.1 s(-1) (K-M = 6 x 10(-9) M). We conclude that the serine P-OH exercises both ground state (GS) destabilization and transition state (TS) stabilization, effects not usually linked to a single residue. With experimental support, we argue that the P-OH destabilizes the GS by imposing conformational constraints on the enzyme and that formation of the TS depends on a rotation of the serine side chain that not only relieves the constraints but brings the P-OH into a position where it can electrostatically stabilize the TS. This rotation would also allow the P-OH to promote both deamination and hydrolysis in the bifunctional deaminases. We find that the E. coli dUTPase does not catalyze the hydrolysis of the alpha,beta-imido-dUTP center dot Mg, suggesting that the analogue provides the hydrogen in the bond to the serine beta-OH. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biochemistry
volume
47
issue
30
pages
7863 - 7874
publisher
The American Chemical Society
external identifiers
  • wos:000257860100012
  • scopus:48249113725
ISSN
0006-2960
DOI
10.1021/bi800325j
language
English
LU publication?
yes
id
94961520-79f8-4e2b-9ffc-828e525fa19a (old id 1253959)
date added to LUP
2008-11-03 15:12:35
date last changed
2017-01-01 04:35:44
@article{94961520-79f8-4e2b-9ffc-828e525fa19a,
  abstract     = {Ser72 at the active site of the Escherichia coli dUTPase has been mutated to an alanine, and the properties of the mutant have been investigated. The serine is absolutely conserved among the monomeric and trimeric dUTPases (including the bifunctional dCTP deaminase:dUTPases), and it has been proposed to promote catalysis by balancing negative charge at the oxygen that bridges the alpha- and beta-pbosphorus of the substrate. In all reported complexes of dUTPases with the substrate analogue alpha,beta-imido-dUTP center dot Mg, the serine beta-OH is indeed hydrogen bonded to the alpha,beta-bridging nitrogen of the analogue. However, in the complex of the Asp90 -> Asn mutant dUTPase with the true substrate dUTP center dot Mg, the serine P-OH points in the opposite direction and may form a hydrogen bond to Asn84 at the bottom of the pyrimidine pocket. Here we show that the replacement of the P-OH by hydrogen reduces k(cat) from 5.8 to 0.008 s(-1) but also k(-1), the rate of substrate dissociation, from 6.2 to 0.1 s(-1) (K-M = 6 x 10(-9) M). We conclude that the serine P-OH exercises both ground state (GS) destabilization and transition state (TS) stabilization, effects not usually linked to a single residue. With experimental support, we argue that the P-OH destabilizes the GS by imposing conformational constraints on the enzyme and that formation of the TS depends on a rotation of the serine side chain that not only relieves the constraints but brings the P-OH into a position where it can electrostatically stabilize the TS. This rotation would also allow the P-OH to promote both deamination and hydrolysis in the bifunctional deaminases. We find that the E. coli dUTPase does not catalyze the hydrolysis of the alpha,beta-imido-dUTP center dot Mg, suggesting that the analogue provides the hydrogen in the bond to the serine beta-OH.},
  author       = {Palmen, Lorena Gonzalez and Becker, Kristian and Bülow, Leif and Kvassman, Jan-Olov},
  issn         = {0006-2960},
  language     = {eng},
  number       = {30},
  pages        = {7863--7874},
  publisher    = {The American Chemical Society},
  series       = {Biochemistry},
  title        = {A double role for a strictly conserved serine: Further insights into the dUTPase catalytic mechanism},
  url          = {http://dx.doi.org/10.1021/bi800325j},
  volume       = {47},
  year         = {2008},
}