4abt

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Current revision (11:23, 20 December 2023) (edit) (undo)
 
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<StructureSection load='4abt' size='340' side='right'caption='[[4abt]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
<StructureSection load='4abt' size='340' side='right'caption='[[4abt]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4abt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"diplococcus_gonorrhoeae"_(zopf_1885)_lehmann_and_neumann_1896 "diplococcus gonorrhoeae" (zopf 1885) lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ABT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ABT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4abt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae Neisseria gonorrhoeae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ABT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ABT FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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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]] 2.22&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fiu|1fiu]]</div></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=CA:CALCIUM+ION'>CA</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=4abt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4abt OCA], [https://pdbe.org/4abt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4abt RCSB], [https://www.ebi.ac.uk/pdbsum/4abt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4abt ProSAT]</span></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=4abt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4abt OCA], [https://pdbe.org/4abt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4abt RCSB], [https://www.ebi.ac.uk/pdbsum/4abt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4abt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/T2M4_NEIGO T2M4_NEIGO]] Recognizes the double-stranded sequence GCCGGC and cleaves after G-1.
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[https://www.uniprot.org/uniprot/T2M4_NEIGO T2M4_NEIGO] Recognizes the double-stranded sequence GCCGGC 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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Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the alpha6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.
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Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.,Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V Nucleic Acids Res. 2012 Apr 11. PMID:22495930<ref>PMID:22495930</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 4abt" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Neisseria gonorrhoeae]]
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[[Category: Golovenko, D]]
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[[Category: Golovenko D]]
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[[Category: Grazulis, S]]
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[[Category: Grazulis S]]
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[[Category: Manakova, E N]]
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[[Category: Manakova EN]]
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[[Category: Siksnys, V]]
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[[Category: Siksnys V]]
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[[Category: Tamulaitiene, G]]
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[[Category: Tamulaitiene G]]
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[[Category: Zaremba, M]]
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[[Category: Zaremba M]]
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[[Category: Hydrolase-dna complex]]
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Current revision

Crystal structure of Type IIF restriction endonuclease NgoMIV with cognate uncleaved DNA

PDB ID 4abt

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