1vrr: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
m Protected "1vrr" [edit=sysop:move=sysop]
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1vrr.png|left|200px]]


<!--
==Crystal structure of the restriction endonuclease BstYI complex with DNA==
The line below this paragraph, containing "STRUCTURE_1vrr", creates the "Structure Box" on the page.
<StructureSection load='1vrr' size='340' side='right'caption='[[1vrr]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1vrr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yuv 1yuv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VRR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</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=1vrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vrr OCA], [https://pdbe.org/1vrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vrr RCSB], [https://www.ebi.ac.uk/pdbsum/1vrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vrr ProSAT]</span></td></tr>
{{STRUCTURE_1vrr|  PDB=1vrr  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q84AF2_GEOSE Q84AF2_GEOSE]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BglII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and BamHI-like elements. Further, DNA recognition is more minimal than BglII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.


===Crystal structure of the restriction endonuclease BstYI complex with DNA===
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.,Townson SA, Samuelson JC, Xu SY, Aggarwal AK Structure. 2005 May;13(5):791-801. PMID:15893669<ref>PMID:15893669</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_15893669}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1vrr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15893669 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15893669}}
__TOC__
 
</StructureSection>
==About this Structure==
[[1vrr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1yuv 1yuv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRR OCA].
 
==Reference==
<ref group="xtra">PMID:015893669</ref><references group="xtra"/>
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Large Structures]]
[[Category: Aggarwal, A K.]]
[[Category: Aggarwal AK]]
[[Category: Samuelson, J C.]]
[[Category: Samuelson JC]]
[[Category: Townson, S A.]]
[[Category: Townson SA]]
[[Category: Xu, S Y.]]
[[Category: Xu SY]]
[[Category: Double helix]]
[[Category: Enzyme-dna complex]]
[[Category: Hydrolase-dna complex]]
Retrieved from "https://proteopedia.org/1vrr"