2vla: Difference between revisions

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-[[Image:2vla.png|left|200px]]
-{{STRUCTURE_2vla|  PDB=2vla  |  SCENE=  }}
+==Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA==
+<StructureSection load='2vla' size='340' side='right'caption='[[2vla]], [[Resolution|resolution]] 1.30&Aring;' 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]] 1.3&#8491;</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.
-===CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BPUJI RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA===
+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>
-{{ABSTRACT_PUBMED_18433771}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2vla" style="background-color:#fffaf0;"></div>
-[[2vla]] is a 3 chain structure of [[Endonuclease]] with sequence from [http://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].
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018433771</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus pumilus]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Large Structures]]
-[[Category: Bochtler, M.]]
+[[Category: Bochtler M]]
-[[Category: Grazulis, S.]]
+[[Category: Grazulis S]]
-[[Category: Siksnys, V.]]
+[[Category: Siksnys V]]
-[[Category: Sukackaite, R.]]
+[[Category: Sukackaite R]]
-[[Category: Dna recognition]]
-[[Category: Endonuclease]]
-[[Category: Helix-turn-helix]]
-[[Category: Hydrolase]]
-[[Category: Restriction endonuclease]]