3bam

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[[Image:3bam.gif|left|200px]]
 
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{{Structure
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==RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)==
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|PDB= 3bam |SIZE=350|CAPTION= <scene name='initialview01'>3bam</scene>, resolution 1.8&Aring;
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<StructureSection load='3bam' size='340' side='right'caption='[[3bam]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>
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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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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bam OCA], [http://www.ebi.ac.uk/pdbsum/3bam PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bam RCSB]</span>
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== Function ==
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}}
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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 ==
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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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'''RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)'''
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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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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 3bam" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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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*[[BamHI|BamHI]]
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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==About this Structure==
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== References ==
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3BAM is a [[Single protein]] structure of sequence from [http://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].
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<references/>
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__TOC__
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==Reference==
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</StructureSection>
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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://www.ncbi.nlm.nih.gov/pubmed/9783752 9783752]
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[[Category: Bacillus amyloliquefaciens]]
[[Category: Bacillus amyloliquefaciens]]
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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: Aggarwal AK]]
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[[Category: Aggarwal, A K.]]
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[[Category: Viadiu H]]
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[[Category: Viadiu, H.]]
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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 Mon Mar 31 05:24:35 2008''
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Current revision

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

PDB ID 3bam

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