2vla: Difference between revisions
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< | ==Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA== | ||
<StructureSection load='2vla' size='340' side='right'caption='[[2vla]], [[Resolution|resolution]] 1.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2vla]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_pumilus Bacillus pumilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLA 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]] 1.3Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene></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=2vla FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vla OCA], [https://pdbe.org/2vla PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vla RCSB], [https://www.ebi.ac.uk/pdbsum/2vla PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vla ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A3FMN7_BACPU A3FMN7_BACPU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence. BpuJI consists of two physically separate domains, with catalytic and dimerization functions in the C-terminal domain and DNA recognition functions in the N-terminal domain. Here we report the crystal structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A resolution. This region folds into two winged-helix subdomains, D1 and D2, interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share structural similarity with the similar subdomains of the FokI DNA-binding domain; however, their orientations in protein-DNA complexes are different. Recognition of the 5'-CCCGT target sequence is achieved by BpuJI through the major groove contacts of amino acid residues located on both the helix-turn-helix motifs and the N-terminal arm. The role of these interactions in DNA recognition is also corroborated by mutational analysis. | |||
The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.,Sukackaite R, Grazulis S, Bochtler M, Siksnys V J Mol Biol. 2008 May 16;378(5):1084-93. Epub 2008 Mar 28. PMID:18433771<ref>PMID:18433771</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vla" style="background-color:#fffaf0;"></div> | |||
== | |||
==See Also== | ==See Also== | ||
*[[Endonuclease|Endonuclease]] | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Bacillus pumilus]] | [[Category: Bacillus pumilus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Bochtler | [[Category: Bochtler M]] | ||
[[Category: Grazulis | [[Category: Grazulis S]] | ||
[[Category: Siksnys | [[Category: Siksnys V]] | ||
[[Category: Sukackaite | [[Category: Sukackaite R]] | ||
Latest revision as of 13:01, 9 May 2024
Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNACrystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA
Structural highlights
FunctionPublication Abstract from PubMedType IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence. BpuJI consists of two physically separate domains, with catalytic and dimerization functions in the C-terminal domain and DNA recognition functions in the N-terminal domain. Here we report the crystal structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A resolution. This region folds into two winged-helix subdomains, D1 and D2, interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share structural similarity with the similar subdomains of the FokI DNA-binding domain; however, their orientations in protein-DNA complexes are different. Recognition of the 5'-CCCGT target sequence is achieved by BpuJI through the major groove contacts of amino acid residues located on both the helix-turn-helix motifs and the N-terminal arm. The role of these interactions in DNA recognition is also corroborated by mutational analysis. The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.,Sukackaite R, Grazulis S, Bochtler M, Siksnys V J Mol Biol. 2008 May 16;378(5):1084-93. Epub 2008 Mar 28. PMID:18433771[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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