2z6q
From Proteopedia
(New page: 200px<br /><applet load="2z6q" size="450" color="white" frame="true" align="right" spinBox="true" caption="2z6q, resolution 2.79Å" /> '''Ternary structure of...) |
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| - | [[Image:2z6q.jpg|left|200px]]<br /><applet load="2z6q" size=" | + | [[Image:2z6q.jpg|left|200px]]<br /><applet load="2z6q" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2z6q, resolution 2.79Å" /> | caption="2z6q, resolution 2.79Å" /> | ||
'''Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy'''<br /> | '''Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2Z6Q is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_parahaemolyticus Haemophilus parahaemolyticus] with DCZ and SAH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] Full crystallographic information is available from [http:// | + | 2Z6Q is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_parahaemolyticus Haemophilus parahaemolyticus] with <scene name='pdbligand=DCZ:'>DCZ</scene> and <scene name='pdbligand=SAH:'>SAH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6Q OCA]. |
==Reference== | ==Reference== | ||
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[[Category: transferase/dna complex]] | [[Category: transferase/dna complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:55:08 2008'' |
Revision as of 11:55, 23 January 2008
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Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy
Overview
Arg165 forms part of a previously identified base flipping motif in the, bacterial DNA cytosine methyltransferase, M.HhaI. Replacement of Arg165, with Ala has no detectable effect on either DNA or AdoMet affinity, yet, causes the base flipping and restacking transitions to be decreased, approximately 16 and 190-fold respectively, thus confirming the importance, of this motif. However, these kinetic changes cannot account for the, mutant's observed 10(5)-fold decreased catalytic rate. The mutant, enzyme/cognate DNA cocrystal structure (2.79 A resolution) shows the, target cytosine to be positioned approximately 30 degrees into the major, groove, which is consistent with a major groove pathway for nucleotide, flipping. The pyrimidine-sugar chi angle is rotated to approximately +171, degrees, from a range of -95 degrees to -120 degrees in B DNA, and -77, degrees in the WT M.HhaI complex. Thus, Arg165 is important for, maintaining the cytosine positioned for nucleophilic attack by Cys81. The, cytosine sugar pucker is in the C2'-endo-C3'-exo (South conformation), in, contrast to the previously reported C3'-endo (North conformation), described for the original 2.70 A resolution cocrystal structure of the WT, M.HhaI/DNA complex. We determined a high resolution structure of the WT, M.HhaI/DNA complex (1.96 A) to better determine the sugar pucker. This new, structure is similar to the original, lower resolution WT M.HhaI complex, but shows that the sugar pucker is O4'-endo (East conformation), intermediate between the South and North conformers. In summary, Arg165, plays significant roles in base flipping, cytosine positioning, and, catalysis. Furthermore, the previously proposed M.HhaI-mediated changes in, sugar pucker may not be an important contributor to the base flipping, mechanism. These results provide insights into the base flipping and, catalytic mechanisms for bacterial and eukaryotic DNA methyltransferases.
About this Structure
2Z6Q is a Single protein structure of sequence from Haemophilus parahaemolyticus with and as ligands. Active as DNA (cytosine-5-)-methyltransferase, with EC number 2.1.1.37 Full crystallographic information is available from OCA.
Reference
The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI., Shieh FK, Youngblood B, Reich NO, J Mol Biol. 2006 Sep 22;362(3):516-27. Epub 2006 Jul 22. PMID:16926025
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