2okv

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[[Image:2okv.gif|left|200px]]<br /><applet load="2okv" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2okv, resolution 2.00&Aring;" />
 
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'''c-Myc DNA Unwinding Element Binding Protein'''<br />
 
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==Overview==
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==c-Myc DNA Unwinding Element Binding Protein==
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Local zones of easily unwound DNA are characteristic of prokaryotic and, eukaryotic replication origins. The DNA-unwinding element of the human, c-myc replication origin is essential for replicator activity and is a, target of the DNA-unwinding element-binding protein DUE-B in vivo. We, present here the 2.0A crystal structure of DUE-B and complementary, biochemical characterization of its biological activity. The structure, corresponds to a dimer of the N-terminal domain of the full-length protein, and contains many of the structural elements of the nucleotide binding, fold. A single magnesium ion resides in the putative active site cavity, which could serve to facilitate ATP hydrolytic activity of this protein., The structure also demonstrates a notable similarity to those of, tRNA-editing enzymes. Consistent with this structural homology, the, N-terminal core of DUE-B is shown to display both d-aminoacyl-tRNA, deacylase activity and ATPase activity. We further demonstrate that the, C-terminal portion of the enzyme is disordered and not essential for, dimerization. However, this region is essential for DNA binding in vitro, and becomes ordered in the presence of DNA.
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<StructureSection load='2okv' size='340' side='right'caption='[[2okv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2okv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OKV 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&#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=MG:MAGNESIUM+ION'>MG</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=2okv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2okv OCA], [https://pdbe.org/2okv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2okv RCSB], [https://www.ebi.ac.uk/pdbsum/2okv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2okv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DTD1_HUMAN DTD1_HUMAN] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (Potential).
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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/ok/2okv_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=2okv 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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Local zones of easily unwound DNA are characteristic of prokaryotic and eukaryotic replication origins. The DNA-unwinding element of the human c-myc replication origin is essential for replicator activity and is a target of the DNA-unwinding element-binding protein DUE-B in vivo. We present here the 2.0A crystal structure of DUE-B and complementary biochemical characterization of its biological activity. The structure corresponds to a dimer of the N-terminal domain of the full-length protein and contains many of the structural elements of the nucleotide binding fold. A single magnesium ion resides in the putative active site cavity, which could serve to facilitate ATP hydrolytic activity of this protein. The structure also demonstrates a notable similarity to those of tRNA-editing enzymes. Consistent with this structural homology, the N-terminal core of DUE-B is shown to display both D-aminoacyl-tRNA deacylase activity and ATPase activity. We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA.
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==About this Structure==
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Structure and function of the c-myc DNA-unwinding element-binding protein DUE-B.,Kemp M, Bae B, Yu JP, Ghosh M, Leffak M, Nair SK J Biol Chem. 2007 Apr 6;282(14):10441-8. Epub 2007 Jan 30. PMID:17264083<ref>PMID:17264083</ref>
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2OKV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKV 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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Structure and Function of the c-myc DNA-unwinding Element-binding Protein DUE-B., Kemp M, Bae B, Yu JP, Ghosh M, Leffak M, Nair SK, J Biol Chem. 2007 Apr 6;282(14):10441-10448. Epub 2007 Jan 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17264083 17264083]
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</div>
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<div class="pdbe-citations 2okv" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bae, B.]]
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[[Category: Bae B]]
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[[Category: Nair, S.K.]]
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[[Category: Nair SK]]
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[[Category: MG]]
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[[Category: atpase]]
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[[Category: dna replication]]
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[[Category: due]]
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[[Category: trna deacylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:32:34 2008''
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Current revision

c-Myc DNA Unwinding Element Binding Protein

PDB ID 2okv

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