5o6g: Difference between revisions
New page: '''Unreleased structure''' The entry 5o6g is ON HOLD Authors: Molina, R., Marcaida, M.J. Description: Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI... |
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==Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI== | |||
<StructureSection load='5o6g' size='340' side='right'caption='[[5o6g]], [[Resolution|resolution]] 2.75Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5o6g]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_mucosus Desulfurococcus mucosus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O6G 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]] 2.75Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5o6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6g OCA], [https://pdbe.org/5o6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o6g RCSB], [https://www.ebi.ac.uk/pdbsum/5o6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6g ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DMO1_DESMO DMO1_DESMO] Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity. | |||
Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.,Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R, D'Abramo M J Comput Aided Mol Des. 2017 Nov 25. pii: 10.1007/s10822-017-0087-5. doi:, 10.1007/s10822-017-0087-5. PMID:29177929<ref>PMID:29177929</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5o6g" style="background-color:#fffaf0;"></div> | ||
[[Category: Marcaida | |||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Desulfurococcus mucosus]] | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Marcaida MJ]] | |||
[[Category: Molina R]] | |||
Latest revision as of 22:09, 29 November 2023
Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoIStructures and dynamics of mesophilic variants from the homing endonuclease I-DmoI
Structural highlights
FunctionDMO1_DESMO Endonuclease involved in intron homing. Recognizes a recognizes up to 20 bp of DNA in the 23S rRNA gene intron. It has a slow turnover rate and cuts the coding strand with a slight preference over the non-coding strand. Publication Abstract from PubMedI-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity. Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.,Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R, D'Abramo M J Comput Aided Mol Des. 2017 Nov 25. pii: 10.1007/s10822-017-0087-5. doi:, 10.1007/s10822-017-0087-5. PMID:29177929[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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