PDBsum entry 1r2y

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Hydrolase/DNA PDB id
Protein chain
273 a.a. *
Waters ×135
* Residue conservation analysis

References listed in PDB file
Key reference
Title Dna lesion recognition by the bacterial repair enzyme mutm.
Authors J.C.Fromme, G.L.Verdine.
Ref. J Biol Chem, 2003, 278, 51543-51548. [DOI no: 10.1074/jbc.M307768200]
PubMed id 14525999
MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA. The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases present in genomic DNA. The crystal structure of a recognition-competent but catalytically inactive version of MutM in complex with oxoG-containing DNA reveals the structural basis for recognition. MutM binds the oxoG nucleoside in the syn glycosidic configuration and distinguishes oxoG from guanine by reading out the protonation state of the N7 atom. The segment of MutM principally responsible for oxoG recognition is a flexible loop, suggesting that conformational mobility influences lesion recognition and catalysis. Furthermore, the structure of MutM in complex with DNA containing an alternative substrate, dihydrouracil, demonstrates how MutM is able to recognize lesions other than oxoG.
Figure 3.
FIG. 3. a, interaction of the Watson-Crick face of oxoG with MutM. b, close-up view of the oxoG recognition complex active site with Glu-3, as determined in a previous study (13) shown in dark gray, superimposed for purposes of comparison with Gln-3 (this study). The approximate locations of main-chain amides involved in hydrogen bonds with Glu-3 are shown as labeled blue circles. Coloring is as in Fig. 1.
Figure 4.
FIG. 4. The dihydrouracil recognition complex. a, stereo view of the active site region, with the final model superimposed on a A-weighted 2F[o] - F[c] electron density map calculated to 1.63 Å using simulated annealing omit phases and contoured at 1.0 . b, superposition of the oxoG and DHU recognition complexes. Coloring as in Fig. 1, except that the dihydrouracil moiety is colored red, and the oxoG nucleoside is dark gray.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 51543-51548) copyright 2003.
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