1yfj

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[[Image:1yfj.gif|left|200px]]<br /><applet load="1yfj" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yfj, resolution 2.69&Aring;" />
 
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'''T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact'''<br />
 
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==Overview==
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==T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact==
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<StructureSection load='1yfj' size='340' side='right'caption='[[1yfj]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yfj]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFJ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.69&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfj OCA], [https://pdbe.org/1yfj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yfj RCSB], [https://www.ebi.ac.uk/pdbsum/1yfj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yfj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DMA_BPT4 DMA_BPT4] This methylase recognizes the double-stranded sequence GATC, causes specific methylation on A-2 on both strands.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yf/1yfj_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1yfj ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.
DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.
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==About this Structure==
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Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.,Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X Cell. 2005 May 6;121(3):349-61. PMID:15882618<ref>PMID:15882618</ref>
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1YFJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=SAH:'>SAH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFJ OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase., Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X, Cell. 2005 May 6;121(3):349-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15882618 15882618]
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</div>
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[[Category: Bacteriophage t4]]
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<div class="pdbe-citations 1yfj" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Site-specific DNA-methyltransferase (adenine-specific)]]
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[[Category: Cheng, X.]]
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[[Category: Hattman, S.]]
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[[Category: Horton, J R.]]
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[[Category: Jeltsch, A.]]
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[[Category: Liebert, K.]]
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[[Category: CA]]
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[[Category: CL]]
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[[Category: SAH]]
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[[Category: dna]]
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[[Category: methyltransferase]]
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[[Category: protein-dna complex]]
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[[Category: t4dam]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:04:47 2008''
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==See Also==
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*[[DNA adenine methylase|DNA adenine methylase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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[[Category: Cheng X]]
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[[Category: Hattman S]]
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[[Category: Horton JR]]
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[[Category: Jeltsch A]]
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[[Category: Liebert K]]

Current revision

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact

PDB ID 1yfj

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