3bam

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[[Image:3bam.gif|left|200px]]<br /><applet load="3bam" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="3bam, resolution 1.8&Aring;" />
 
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'''RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)'''<br />
 
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==Overview==
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==RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)==
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<StructureSection load='3bam' size='340' side='right'caption='[[3bam]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3bam]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BAM 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]] 1.8&#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=MN:MANGANESE+(II)+ION'>MN</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=3bam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bam OCA], [https://pdbe.org/3bam PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bam RCSB], [https://www.ebi.ac.uk/pdbsum/3bam PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bam ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/T2BA_BACAM T2BA_BACAM] Recognizes the double-stranded sequence GGATCC and cleaves after G-1.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage. Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.
Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage. Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.
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==About this Structure==
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The role of metals in catalysis by the restriction endonuclease BamHI.,Viadiu H, Aggarwal AK Nat Struct Biol. 1998 Oct;5(10):910-6. PMID:9783752<ref>PMID:9783752</ref>
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3BAM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=3BAM 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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The role of metals in catalysis by the restriction endonuclease BamHI., Viadiu H, Aggarwal AK, Nat Struct Biol. 1998 Oct;5(10):910-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9783752 9783752]
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</div>
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[[Category: Bacillus amyloliquefaciens]]
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<div class="pdbe-citations 3bam" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Aggarwal, A K.]]
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[[Category: Viadiu, H.]]
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[[Category: MN]]
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[[Category: complex (endonuclease/dna)]]
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[[Category: hydrolase]]
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[[Category: nuclease]]
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[[Category: phosphodiesterase]]
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[[Category: protein/dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:04:28 2008''
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==See Also==
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*[[BamHI|BamHI]]
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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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: Bacillus amyloliquefaciens]]
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[[Category: Large Structures]]
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[[Category: Aggarwal AK]]
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[[Category: Viadiu H]]

Current revision

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)

PDB ID 3bam

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