2oxv: Difference between revisions

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OCA

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-[[Image:2oxv.gif|left|200px]]<br /><applet load="2oxv" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2oxv, resolution 1.950&Aring;" />
-'''Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site.'''<br />
-==Overview==
+==Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site.==
-Promiscuous mutant EcoRI endonucleases bind to the canonical site GAATTC, more tightly than does the wild-type endonuclease, yet cleave variant, (EcoRI(*)) sites more rapidly than does wild-type. The crystal structure, of the A138T promiscuous mutant homodimer in complex with a GAATTC site is, nearly identical to that of the wild-type complex, except that the Thr138, side chains make packing interactions with bases in the 5'-flanking, regions outside the recognition hexanucleotide while excluding two bound, water molecules seen in the wild-type complex. Molecular dynamics, simulations confirm exclusion of these waters. The structure and, simulations suggest possible reasons why binding of the A138T protein to, the GAATTC site has DeltaS degrees more favorable and DeltaH degrees less, favorable than for wild-type endonuclease binding. The interactions of, Thr138 with flanking bases may permit A138T, unlike wild-type enzyme, to, form complexes with EcoRI(*) sites that structurally resemble the specific, wild-type complex with GAATTC.
+<StructureSection load='2oxv' size='340' side='right'caption='[[2oxv]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2oxv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXV 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]] 1.95&#8491;</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=2oxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxv OCA], [https://pdbe.org/2oxv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxv RCSB], [https://www.ebi.ac.uk/pdbsum/2oxv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/T2E1_ECOLX T2E1_ECOLX] Recognizes the double-stranded sequence GAATTC and cleaves after G-1.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Promiscuous mutant EcoRI endonucleases bind to the canonical site GAATTC more tightly than does the wild-type endonuclease, yet cleave variant (EcoRI(*)) sites more rapidly than does wild-type. The crystal structure of the A138T promiscuous mutant homodimer in complex with a GAATTC site is nearly identical to that of the wild-type complex, except that the Thr138 side chains make packing interactions with bases in the 5'-flanking regions outside the recognition hexanucleotide while excluding two bound water molecules seen in the wild-type complex. Molecular dynamics simulations confirm exclusion of these waters. The structure and simulations suggest possible reasons why binding of the A138T protein to the GAATTC site has DeltaS degrees more favorable and DeltaH degrees less favorable than for wild-type endonuclease binding. The interactions of Thr138 with flanking bases may permit A138T, unlike wild-type enzyme, to form complexes with EcoRI(*) sites that structurally resemble the specific wild-type complex with GAATTC.
-==About this Structure==
+Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease.,Sapienza PJ, Rosenberg JM, Jen-Jacobson L Structure. 2007 Nov;15(11):1368-82. PMID:17997963<ref>PMID:17997963</ref>
-OXV is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXV OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease., Sapienza PJ, Rosenberg JM, Jen-Jacobson L, Structure. 2007 Nov;15(11):1368-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17997963 17997963]
+</div>
+<div class="pdbe-citations 2oxv" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Jen-Jacobson L]]
-[[Category: Jen-Jacobson, L.]]
+[[Category: Rosenberg JM]]
-[[Category: Rosenberg, J.M.]]
+[[Category: Sapienza PJ]]
-[[Category: Sapienza, P.J.]]
-[[Category: ecori]]
-[[Category: hydrolase/dna complex]]
-[[Category: promiscuous mutant]]
-[[Category: protein-dna interactions]]
-[[Category: relaxed specificity mutant]]
-[[Category: type ii restriction endonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:39:53 2008''