1yfj

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{{Seed}}
 
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[[Image:1yfj.png|left|200px]]
 
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==T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact==
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The line below this paragraph, containing "STRUCTURE_1yfj", creates the "Structure Box" on the page.
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<StructureSection load='1yfj' size='340' side='right'caption='[[1yfj]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_1yfj| PDB=1yfj | SCENE= }}
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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 ==
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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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===T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact===
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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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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1yfj" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15882618}}, adds the Publication Abstract to the page
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*[[DNA adenine methylase|DNA adenine methylase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15882618 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15882618}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia virus T4]]
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1YFJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFJ OCA].
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[[Category: Large Structures]]
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[[Category: Cheng X]]
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==Reference==
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[[Category: Hattman S]]
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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://www.ncbi.nlm.nih.gov/pubmed/15882618 15882618]
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[[Category: Horton JR]]
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[[Category: Enterobacteria phage t4]]
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[[Category: Jeltsch A]]
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[[Category: Single protein]]
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[[Category: Liebert K]]
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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: Dna,protein-dna complex]]
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[[Category: Methyltransferase]]
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[[Category: T4dam]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 12:07:01 2008''
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Current revision

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

PDB ID 1yfj

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