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4qbf

From Proteopedia

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Current revision

Crystal structure of a stable adenylate kinase variant AKlse2

Structural highlights

4qbf is a 1 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4qbf"

Categories: Bacillus subtilis subsp. subtilis str. 168 | Large Structures | Bae E | Moon S

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <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" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</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]] 1.8&#8491;</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='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>
 </table>

4qbf

From Proteopedia

Current revision

Crystal structure of a stable adenylate kinase variant AKlse2

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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