2hr1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2hr1" size="450" color="white" frame="true" align="right" spinBox="true" caption="2hr1, resolution 1.96&Aring;" /> '''Ternary structure of...)
Current revision (09:34, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2hr1.gif|left|200px]]<br /><applet load="2hr1" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2hr1, resolution 1.96&Aring;" />
 
-
'''Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy'''<br />
 
-
==Overview==
+
==Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy==
-
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.
+
<StructureSection load='2hr1' size='340' side='right'caption='[[2hr1]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2hr1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_parahaemolyticus Haemophilus parahaemolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HR1 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hr1 OCA], [https://pdbe.org/2hr1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hr1 RCSB], [https://www.ebi.ac.uk/pdbsum/2hr1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hr1 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/MTH1_HAEPH MTH1_HAEPH] This methylase recognizes the double-stranded sequence GCGC, causes specific methylation on C-2 on both strands, and protects the DNA from cleavage by the HhaI endonuclease.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/2hr1_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2hr1 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2HR1 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 SAH as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deleted_entry Deleted entry], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.73 2.1.1.73] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2HR1 OCA].
+
*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16926025 16926025]
+
-
[[Category: Deleted entry]]
+
[[Category: Haemophilus parahaemolyticus]]
[[Category: Haemophilus parahaemolyticus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Shieh, F.]]
+
[[Category: Shieh F]]
-
[[Category: SAH]]
+
-
[[Category: high resolution]]
+
-
[[Category: m.hhai]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:55:24 2007''
+

Current revision

Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy

PDB ID 2hr1

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hr1"
Personal tools