1b97: Difference between revisions

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-{{Seed}}
-[[Image:1b97.png|left|200px]]
-<!--
+==ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP==
-The line below this paragraph, containing "STRUCTURE_1b97", creates the "Structure Box" on the page.
+<StructureSection load='1b97' size='340' side='right'caption='[[1b97]], [[Resolution|resolution]] 1.90&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'>[[1b97]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B97 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]] 1.9&#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=1b97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b97 OCA], [https://pdbe.org/1b97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b97 RCSB], [https://www.ebi.ac.uk/pdbsum/1b97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b97 ProSAT]</span></td></tr>
-{{STRUCTURE_1b97|  PDB=1b97  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Following random mutagenesis of the Eco RV endonuclease, a high proportion of the null mutants carry substitutions at Gln69. Such mutants display reduced rates for the DNA cleavage step in the reaction pathway, yet the crystal structures of wild-type Eco RV fail to explain why Gln69 is crucial for activity. In this study, crystal structures were determined for two mutants of Eco RV, with Leu or Glu at residue 69, bound to specific DNA. The structures of the mutants are similar to the native protein and no function can be ascribed to the side chain of the amino acid at this locus. Instead, the structures of the mutant proteins suggest that the catalytic defect is due to the positioning of the main chain carbonyl group. In the enzyme-substrate complex for Eco RV, the main chain carbonyl of Gln69 makes no interactions with catalytic functions but, in the enzyme-product complex, it coordinates a metal ion bound to the newly liberated 5'-phosphate. This re-positioning may be hindered in the mutant proteins. Molecular dynamics calculations indicate that the metal on the phosphoryl oxygen interacts with the carbonyl group upon forming the pentavalent intermediate during phosphodiester hydrolysis. A main chain carbonyl may thus play a role in catalysis by Eco RV.
-===ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP===
+Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group.,Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS Nucleic Acids Res. 1999 Sep 1;27(17):3438-45. PMID:10446231<ref>PMID:10446231</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1b97" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10446231}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10446231 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10446231}}
+__TOC__
+</StructureSection>
-==About this Structure==
-B97 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B97 OCA].
-==Reference==
-Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group., Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS, Nucleic Acids Res. 1999 Sep 1;27(17):3438-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10446231 10446231]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Brady RL]]
-[[Category: Brady, R L.]]
+[[Category: Halford SE]]
-[[Category: Halford, S E.]]
+[[Category: Thomas MP]]
-[[Category: Thomas, M P.]]
-[[Category: Ecorv]]
-[[Category: Endonuclease]]
-[[Category: Restriction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 18:36:45 2008''