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PDB ID Mentions in PubMed Central Article count: 2

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PDB ID Mentions in PubMed Central

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Modern aspects of the structural and functional organization of the DNA mismatch repair system.

(2013) Acta Naturae 5

PubMed: 24303200 | PubMedCentral: PMC3848065 | DOI: null

Table 2 Crystal structures of the MutS protein Organism DNA 1 ATP or ADP Resolution, A ° PDB code Reference Substitution, aa E. coli 2 G/T ADP 2.20 1E3M [55] - « « 2.10 1WB9 [8... ] E38T « « 2.50 1WBB [84] E38A « « 2.40 1WBD [84] E38Q « « 2.20 3K0S [83] D693N « ADP (2 molecules) 2.60 1NG9 [79] R697A « ADP (2 molecules) 2.27 1W7A [85] - A/A ADP 2.40 1OH6 [81] - A/A « 3.40 2WTU [83] - G/G « 2.50 1OH7 [81] - C/A « 2.90 1OH5 [81] - extra T « 2.90 1OH8 [81] - Thermus aquaticus 3 - - 3.19 1EWR [78] - extra T - 2.20 1EWQ [78] - extra T ADP (2 molecules) 2.70 1FW6 [79] - extra T ADP (2 molecules)·BeF 3 3.11 1NNE [82] - Human (MSHα) G/T ADP 3.30 2O8E [86] - G/T ADP (2 molecules) 2.75 2O8B « - G/dU ADP 3.00 2O8D « - m 6 G/T 4 « 3.37 2O8C « - extra T « 3.25 2O8F « - Human (MSHβ) loop 4 n.r. 5 « 3.09 3THW - - loop 3 n.r. « 2.70 3THX - - loop 2 n.r. « 2.89 3THY - - loop 6 n.r. « 4.30 3THZ - - 1 Non-canonical pair of nucleotides in the DNA duplex used for crystallization is shown.

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4417165

The reasons are multiple: (i) there is no consensus ranking of MutS susceptibility of the different MMs, and (ii) analysis of available X-Ray complexes of mismatched DNA bound to MutS (or MutSα... ) (PDB ids: 1W7A ( 64 ), 2WTU ( 61 ), 1OH5 ( 62 ), 1OH6 ( 62 ), 1OH7 ( 62 ), 1OH8 ( 62 ) and 2O8B ( 66 )) suggests that not only indirect, but also direct recognition mechanisms play a role in defining MutS preferences.

Structural models of mismatched DNA bound to MutS (or MutSα) suggested a syn conformation every time a purine is present in the Crick strand (A·A MM: 2WTU ( 61 ) and 1OH6 ( 62 ); C·A MM: 1OH5 ( 62 ), and G·G/G·8oxoG MMs: 1OH7 ( 62 ) and 1N2W ( 63 ) respectively), while the two MM bases are found in anti when thymine are present, as in the Crick strand of the G·T MM (1W7A ( 64 ), 1OH8 ( 62 ), 1E3M ( 65 ), and 2O8B ( 66 )); on the contrary, available NMR structures of naked-DNA with point mutations (T·G (1KKW ( 67 ) and 1PIB ( 68 )); G·T (1BJD ( 69 ) and 113D ( 70 )); C·T (1FKY ( 71 )), C·C; (1FKZ ( 71 )) and A·G (1ONM ( 72 )) MMs) show both bases are in anti , in agreement with the X-ray structure of C·A and A·C pairs (1D99 ( 70 )).

Publication Year: 2015