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| | <StructureSection load='4qbf' size='340' side='right'caption='[[4qbf]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='4qbf' size='340' side='right'caption='[[4qbf]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4qbf]] is a 1 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=4QBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4qbf]] 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=4QBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBF 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=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </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=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qbg|4qbg]], [[4qbh|4qbh]], [[4qbi|4qbi]]</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=4qbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbf OCA], [https://pdbe.org/4qbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qbf RCSB], [https://www.ebi.ac.uk/pdbsum/4qbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbf ProSAT]</span></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='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=4qbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbf OCA], [http://pdbe.org/4qbf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbf RCSB], [http://www.ebi.ac.uk/pdbsum/4qbf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbf 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adenylate kinase]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Bacsu]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bae, E]] | + | [[Category: Bae E]] |
| - | [[Category: Moon, S]] | + | [[Category: Moon S]] |
| - | [[Category: Atp binding]]
| + | |
| - | [[Category: Phosphorylation]]
| + | |
| - | [[Category: Phosphotransferase activity]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[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
Local structural entropy (LSE) is a descriptor for the extent of conformational heterogeneity in short protein sequences that is computed from structural information derived from the Protein Data Bank. Reducing the LSE of a protein sequence by introducing amino acid mutations can result in fewer conformational states and thus a more stable structure, indicating that LSE optimization can be used as a protein stabilization method. Here, we describe a series of LSE optimization experiments designed to stabilize mesophilic and thermophilic adenylate kinases (AKs) and report crystal structures of LSE-optimized AK variants. In the mesophilic AK, thermal stabilization by LSE reduction was effective but limited. Structural analyses of the LSE-optimized mesophilic AK variants revealed a strong correlation between LSE and the apolar buried surface area. Additional mutations designed to introduce non-covalent interactions between distant regions of the polypeptide resulted in further stabilization. Unexpectedly, optimizing the LSE of the thermophilic AK resulted in a decrease in thermal stability. This destabilization was reduced when charged residues were excluded from the possible substitutions during LSE optimization. These observations suggest that stabilization by LSE reduction may result from the optimization of local hydrophobic contacts. The limitations of this process are likely due to ignorance of other interactions that bridge distant regions in a given amino acid sequence. Our results illustrate the effectiveness and limitations of LSE optimization as a protein stabilization strategy and highlight the importance and complementarity of local conformational stability and global interactions in protein thermal stability. (c) Proteins 2014;. (c) 2014 Wiley Periodicals, Inc.
Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases.,Moon S, Bannen RM, Rutkoski TJ, Phillips GN Jr, Bae E Proteins. 2014 Jun 13. doi: 10.1002/prot.24627. PMID:24931334[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Moon S, Bannen RM, Rutkoski TJ, Phillips GN Jr, Bae E. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins. 2014 Jun 13. doi: 10.1002/prot.24627. PMID:24931334 doi:http://dx.doi.org/10.1002/prot.24627
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