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Table 3 Mechanistic model of the PRR pathway in budding yeast

From: In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae

Reaction Reagents Products Constantc i [sec−1] Reference Step in Figure1
1 P C N A+L P C N A on 1.5 ×10−8 This study c
2 R a d 18+R a d 18 R a d 18:R a d 18 1 ×10−2 [55, 56]  
3 R a d 18:R a d 18 R a d 18+R a d 18 1 ×103 [55, 56]  
4 R a d 6+U R a d 6:U 2.5 ×10−7 [57]  
5 P C N Aon+R a d 18:R a d 18 R a d 18:R a d 18:P C N Aon 1 ×105 [25, 36] d
6 R a d 18:R a d 18:P C N Aon P C N Aon+R a d 18:R a d 18 1 ×103 [25, 36]  
7 R a d 6:U+R a d 18:R a d 18:P C N Aon R a d 18:R a d 18:P C N Aon:R a d 6:U 3.51 ×10−2 [25, 36, 5861], this study  
8 R a d 18:R a d 18:P C N Aon:R a d 6:U R a d 6:U+R a d 18:R a d 18:P C N Aon 1 ×10−2 [25, 36, 5861], this study  
9 R a d 18:R a d 18:P C N Aon:R a d 6:U R a d 6+R a d 18:R a d 18:P C N Aon:U 1 ×10−2 [25, 36, 60] e
10 R a d 18:R a d 18:P C N Aon:U R a d 18:R a d 18+P C N Aon:U 1 [25, 36, 60] e, f
11 U b c 13:M m s 2+U U b c 13:U:M m s 2 1 ×105 [35, 62, 63], this study i
12 P C N Aon:U+R a d 5 R a d 5:P C N Aon:U 5 ×10−6 [36] h
13 R a d 5:P C N Aon:U P C N Aon:U+R a d 5 5 ×10−3 [36] h
14 U b c 13:U:M m s 2+R a d 5:P C N Aon:U U b c 13:U:M m s 2:R a d 5:P C N Aon:U 7.8 ×10−2 [25, 36, 58, 62], this study i
15 U b c 13:U:M m s 2:R a d 5:P C N Aon:U R a d 5:P C N Aon:U+U b c 13:U:M m s 2 1 ×10−10 [25, 36, 58, 62] i
16 U b c 13:U:M m s 2:R a d 5:P C N Aon:U U b c 13:M m s 2+R a d 5:P C N Aon:U:U 5 ×10−2 [36, 54, 63, 64] j, k
17 R a d 5:P C N Aon:U:U R a d 5+P C N Aon:U:U 7.5 ×10−6 This study k
18 P C N Aon:U:U+R a d 5 R a d 5:P C N Aon:U:U 5 ×10−6 This study -
19 U b c 13:U:M m s 2+R a d 5:P C N Aon:U:U U b c 13:U:M m s 2:R a d 5:P C N Aon:U:U 7.8 ×10−2 [25, 36, 58, 62], this study -
20 U b c 13:U:M m s 2:R a d 5:P C N Aon:U:U R a d 5:P C N Aon:U:U+U b c 13:U:M m s 2 1 ×10−10 [25, 36, 58, 62] -
21 U b c 13:U:M m s 2:R a d 5:P C N Aon:U:U U b c 13:M m s 2+R a d 5:P C N Aon:U:U:U 5 ×10−3 [36, 54, 63, 64] l
22 R a d 5:P C N Aon:U:U:U R a d 5+P C N Aon:U:U:U 5 ×10−3 This study l
23 P C N Aon:U U+P C N Aoff 3 ×10−8 This study g
24 P C N Aon:U:U U+U+P C N Aoff 8 ×10−4 This study n
25 P C N Aon:U:U:U U+U+U+P C N Aoff 5 ×10−3 This study m
  1. The mechanistic model for the PRR pathway, developed according to the stochastic formulation of chemical kinetics, consists of 25 reactions among 23 molecular species. Each reaction is described by a set of reagents and a set of products, and is characterized by a stochastic constant (ci, i=1, …, 25), here expressed in sec-1. The following notation was used in writing the reactions: (i) X + Y represents an interaction between the molecular species X and Y; (ii) X : Y describes a molecular complex between species X and Y. Data reported in the fifth column specify the literature references from which we retrieved the information used to define the corresponding reaction. Labels given in the last column associate each reaction to the main steps of the PRR pathway that are graphically represented in Figure 1.