3bvq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:52, 25 October 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3bvq.png|left|200px]]
 
-
<!--
+
==Crystal Structure of Apo NotI Restriction Endonuclease==
-
The line below this paragraph, containing "STRUCTURE_3bvq", creates the "Structure Box" on the page.
+
<StructureSection load='3bvq' size='340' side='right'caption='[[3bvq]], [[Resolution|resolution]] 2.80&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'>[[3bvq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nocardia_otitidiscaviarum Nocardia otitidiscaviarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BVQ 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]] 2.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_3bvq| PDB=3bvq | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvq OCA], [https://pdbe.org/3bvq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvq RCSB], [https://www.ebi.ac.uk/pdbsum/3bvq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvq ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q2I6W2_9NOCA Q2I6W2_9NOCA]
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp target 5'-GCGGCCGC-3', has been solved with and without bound DNA. Because of its specificity (recognizing a site that occurs once per 65 kb), NotI is used to generate large genomic fragments and to map DNA methylation status. NotI contains a unique metal binding fold, found in a variety of putative endonucleases, occupied by an iron atom coordinated within a tetrahedral Cys4 motif. This domain positions nearby protein elements for DNA recognition, and serves a structural role. While recognition of the central six base pairs of the target is accomplished via a saturated hydrogen bond network typical of restriction enzymes, the most peripheral base pairs are engaged in a single direct contact in the major groove, reflecting reduced pressure to recognize those positions. NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases.
-
===Crystal Structure of Apo NotI Restriction Endonuclease===
+
Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.,Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu SY, Stoddard BL Structure. 2008 Apr;16(4):558-69. PMID:18400177<ref>PMID:18400177</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3bvq" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18400177}}, adds the Publication Abstract to the page
+
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18400177 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18400177}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3BVQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Nocardia_otitidiscaviarum Nocardia otitidiscaviarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVQ OCA].
+
-
 
+
-
==Reference==
+
-
Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding., Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu SY, Stoddard BL, Structure. 2008 Apr;16(4):558-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18400177 18400177]
+
[[Category: Nocardia otitidiscaviarum]]
[[Category: Nocardia otitidiscaviarum]]
-
[[Category: Single protein]]
+
[[Category: Lambert AR]]
-
[[Category: Lambert, A R.]]
+
[[Category: Shen B]]
-
[[Category: Shen, B.]]
+
[[Category: Stoddard BL]]
-
[[Category: Stoddard, B L.]]
+
[[Category: Sussman D]]
-
[[Category: Sussman, D.]]
+
-
[[Category: Fe-cys4 motif]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Iron-sulfur protein]]
+
-
[[Category: Rare-cutting]]
+
-
[[Category: Restriction endonuclease]]
+
-
[[Category: Restriction enzyme fold]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:12:41 2008''
+

Current revision

Crystal Structure of Apo NotI Restriction Endonuclease

PDB ID 3bvq

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bvq"
Personal tools