2ore | pdb_00002ore
Binary Structure of Escherichia coli DNA Adenine Methyltransferase and S-adenosylhomocysteine
Structural highlights
Function[DMA_ECOLI] Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of the Escherichia coli DNA adenine methyltransferase (EcoDam) in a binary complex with the cofactor product S-adenosyl-L-homocysteine (AdoHcy) unexpectedly showed the bound AdoHcy in two alternative conformations, extended or folded. The extended conformation represents the catalytically competent conformation, identical to that of EcoDam-DNA-AdoHcy ternary complex. The folded conformation prevents catalysis, because the homocysteine moiety occupies the target Ade binding pocket. The largest difference between the binary and ternary structures is in the conformation of the N-terminal hexapeptide ((9)KWAGGK(14)). Cofactor binding leads to a strong change in the fluorescence of Trp(10), whose indole ring approaches the cofactor by 3.3A(.) Stopped-flow kinetics and AdoMet cross-linking studies indicate that the cofactor prefers binding to the enzyme after preincubation with DNA. In the presence of DNA, AdoMet binding is approximately 2-fold stronger than AdoHcy binding. In the binary complex the side chain of Lys(14) is disordered, whereas Lys(14) stabilizes the active site in the ternary complex. Fluorescence stopped-flow experiments indicate that Lys(14) is important for EcoDam binding of the extrahelical target base into the active site pocket. This suggests that the hexapeptide couples specific DNA binding (Lys(9)), AdoMet binding (Trp(10)), and insertion of the flipped target base into the active site pocket (Lys(14)). Two alternative conformations of S-adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle.,Liebert K, Horton JR, Chahar S, Orwick M, Cheng X, Jeltsch A J Biol Chem. 2007 Aug 3;282(31):22848-55. Epub 2007 May 31. PMID:17545164[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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