1bua

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[[Image:1bua.gif|left|200px]]
 
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{{Structure
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==STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE==
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|PDB= 1bua |SIZE=350|CAPTION= <scene name='initialview01'>1bua</scene>, resolution 2.15&Aring;
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<StructureSection load='1bua' size='340' side='right'caption='[[1bua]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1bua]] is a 4 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=1BUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUA FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.15&#8491;</td></tr>
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|GENE=
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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=1bua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bua OCA], [https://pdbe.org/1bua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bua RCSB], [https://www.ebi.ac.uk/pdbsum/1bua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bua ProSAT]</span></td></tr>
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}}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.
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'''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''
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Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.,Martin AM, Sam MD, Reich NO, Perona JJ Nat Struct Biol. 1999 Mar;6(3):269-77. PMID:10074946<ref>PMID:10074946</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 1bua" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1BUA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUA OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease., Martin AM, Sam MD, Reich NO, Perona JJ, Nat Struct Biol. 1999 Mar;6(3):269-77. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10074946 10074946]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Martin AM]]
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[[Category: Martin, A M.]]
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[[Category: Perona JJ]]
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[[Category: Perona, J J.]]
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[[Category: endonuclease ecorv (e c.3 1.21 4)/dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:15:52 2008''
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Current revision

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE

PDB ID 1bua

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