4mkh: Difference between revisions
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==Crystal structure of a stable adenylate kinase variant AKv18== | ==Crystal structure of a stable adenylate kinase variant AKv18== | ||
<StructureSection load='4mkh' size='340' side='right'caption='[[4mkh]]' scene=''> | <StructureSection load='4mkh' size='340' side='right'caption='[[4mkh]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MKH FirstGlance]. <br> | <table><tr><td colspan='2'>[[4mkh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MKH FirstGlance]. <br> | ||
</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=4mkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mkh OCA], [https://pdbe.org/4mkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mkh RCSB], [https://www.ebi.ac.uk/pdbsum/4mkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mkh ProSAT]</span></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]] 1.5Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4mkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mkh OCA], [https://pdbe.org/4mkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mkh RCSB], [https://www.ebi.ac.uk/pdbsum/4mkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mkh ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/KAD_BACSU KAD_BACSU] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Thermally stable proteins are desirable for research and industrial purposes, but redesigning proteins for higher thermal stability can be challenging. A number of different techniques have been used to improve the thermal stability of proteins, but the extents of stability enhancement were sometimes unpredictable and not significant. Here, we systematically tested the effects of multiple stabilization techniques including a bioinformatic method and structure-guided mutagenesis on a single protein, thereby providing an integrated approach to protein thermal stabilization. Using a mesophilic adenylate kinase (AK) as a model, we identified stabilizing mutations based on various stabilization techniques, and generated a series of AK variants by introducing mutations both individually and collectively. The redesigned proteins displayed a range of increased thermal stabilities, the most stable of which was comparable to a naturally evolved thermophilic homologue with more than a 25 degrees increase in its thermal denaturation midpoint. We also solved crystal structures of three representative variants including the most stable variant, to confirm the structural basis for their increased stabilities. These results provide a unique opportunity for systematically analyzing the effectiveness and additivity of various stabilization mechanisms, and they represent a useful approach for improving protein stability by integrating the reduction of local structural entropy and the optimization of global noncovalent interactions such as hydrophobic contact and ion pairs. Proteins 2014. (c) 2014 Wiley Periodicals, Inc. | |||
An integrated approach for thermal stabilization of a mesophilic adenylate kinase.,Moon S, Jung DK, Phillips GN Jr, Bae E Proteins. 2014 Mar 11. doi: 10.1002/prot.24549. PMID:24615904<ref>PMID:24615904</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4mkh" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] | *[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus subtilis subsp. subtilis str. 168]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bae E]] | [[Category: Bae E]] | ||
[[Category: Moon S]] | [[Category: Moon S]] | ||
Latest revision as of 17:43, 8 November 2023
Crystal structure of a stable adenylate kinase variant AKv18Crystal structure of a stable adenylate kinase variant AKv18
Structural highlights
FunctionKAD_BACSU Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. Publication Abstract from PubMedThermally stable proteins are desirable for research and industrial purposes, but redesigning proteins for higher thermal stability can be challenging. A number of different techniques have been used to improve the thermal stability of proteins, but the extents of stability enhancement were sometimes unpredictable and not significant. Here, we systematically tested the effects of multiple stabilization techniques including a bioinformatic method and structure-guided mutagenesis on a single protein, thereby providing an integrated approach to protein thermal stabilization. Using a mesophilic adenylate kinase (AK) as a model, we identified stabilizing mutations based on various stabilization techniques, and generated a series of AK variants by introducing mutations both individually and collectively. The redesigned proteins displayed a range of increased thermal stabilities, the most stable of which was comparable to a naturally evolved thermophilic homologue with more than a 25 degrees increase in its thermal denaturation midpoint. We also solved crystal structures of three representative variants including the most stable variant, to confirm the structural basis for their increased stabilities. These results provide a unique opportunity for systematically analyzing the effectiveness and additivity of various stabilization mechanisms, and they represent a useful approach for improving protein stability by integrating the reduction of local structural entropy and the optimization of global noncovalent interactions such as hydrophobic contact and ion pairs. Proteins 2014. (c) 2014 Wiley Periodicals, Inc. An integrated approach for thermal stabilization of a mesophilic adenylate kinase.,Moon S, Jung DK, Phillips GN Jr, Bae E Proteins. 2014 Mar 11. doi: 10.1002/prot.24549. PMID:24615904[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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