|
|
| Line 3: |
Line 3: |
| | <StructureSection load='1b97' size='340' side='right'caption='[[1b97]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='1b97' size='340' side='right'caption='[[1b97]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1b97]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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> | + | <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> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECORVR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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> | | <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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
| + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 26: |
Line 25: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[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: Hydrolase-dna complex]]
| + | |
| - | [[Category: Restriction]]
| + | |
| Structural highlights
Function
T2E5_ECOLX Recognizes the double-stranded sequence GATATC and cleaves after T-3.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS. Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group. Nucleic Acids Res. 1999 Sep 1;27(17):3438-45. PMID:10446231
|
