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| | ==Crystal structure of a stable adenylate kinase variant AKv3== | | ==Crystal structure of a stable adenylate kinase variant AKv3== |
| - | <StructureSection load='4mkf' size='340' side='right' caption='[[4mkf]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='4mkf' size='340' side='right'caption='[[4mkf]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mkf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MKF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MKF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mkf]] is a 2 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=4MKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MKF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mkg|4mkg]], [[4mkh|4mkh]]</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adk, BSU01370 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4mkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mkf OCA], [https://pdbe.org/4mkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mkf RCSB], [https://www.ebi.ac.uk/pdbsum/4mkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mkf ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mkf OCA], [http://pdbe.org/4mkf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mkf RCSB], [http://www.ebi.ac.uk/pdbsum/4mkf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mkf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4mkf" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4mkf" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] |
| | + | *[[BRCA 3D structures|BRCA 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adenylate kinase]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Bacsu]] | + | [[Category: Large Structures]] |
| - | [[Category: Bae, E]] | + | [[Category: Bae E]] |
| - | [[Category: Jung, D]] | + | [[Category: Jung D]] |
| - | [[Category: Moon, S]] | + | [[Category: Moon S]] |
| - | [[Category: Atp binding]]
| + | |
| - | [[Category: Phosphorylation]]
| + | |
| - | [[Category: Phosphotransferase activity]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transferase activity]]
| + | |
| - | [[Category: Zinc binding]]
| + | |
| - | [[Category: Zinc finger]]
| + | |
| Structural highlights
Function
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Moon S, Jung DK, Phillips GN Jr, Bae E. An integrated approach for thermal stabilization of a mesophilic adenylate kinase. Proteins. 2014 Mar 11. doi: 10.1002/prot.24549. PMID:24615904 doi:http://dx.doi.org/10.1002/prot.24549
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