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| | <StructureSection load='5xzi' size='340' side='right'caption='[[5xzi]], [[Resolution|resolution]] 2.65Å' scene=''> | | <StructureSection load='5xzi' size='340' side='right'caption='[[5xzi]], [[Resolution|resolution]] 2.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5xzi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xzi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XZI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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]] 2.65Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cybC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=HEC:HEME+C'>HEC</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzi OCA], [http://pdbe.org/5xzi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xzi RCSB], [http://www.ebi.ac.uk/pdbsum/5xzi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzi ProSAT]</span></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=5xzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xzi OCA], [https://pdbe.org/5xzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xzi RCSB], [https://www.ebi.ac.uk/pdbsum/5xzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xzi ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function. | + | [https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function. |
| | <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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Song, W J]] | + | [[Category: Song WJ]] |
| - | [[Category: Tezcan, F A]] | + | [[Category: Tezcan FA]] |
| - | [[Category: De novo protein]]
| + | |
| - | [[Category: Electron transport]]
| + | |
| Structural highlights
Function
C562_ECOLX Electron-transport protein of unknown function.
Publication Abstract from PubMed
We describe the design and evolution of catalytic hydrolase activity on a supramolecular protein scaffold, Zn4:(C96)RIDC14, which was constructed from cytochrome cb562 building blocks via a metal-templating strategy. Previously, we reported that Zn4:(C96)RIDC14 could be tailored with tripodal (His/His/Glu), unsaturated Zn coordination motifs in its interfaces to generate a variant termed Zn8:(A104)AB34, which in turn displayed catalytic activity for the hydrolysis of activated esters and beta-lactam antibiotics. Zn8:(A104)AB34 was subsequently subjected to directed evolution via an in vivo selection strategy, leading to a variant Zn8:(A104/G57)AB34 which displayed enzyme-like Michaelis-Menten behavior for ampicillin hydrolysis. A criterion for the evolutionary utility or designability of a new protein structure is its ability to accommodate different active sites. With this in mind, we examined whether Zn4:(C96)RIDC14 could be tailored with alternative Zn coordination sites that could similarly display evolvable catalytic activities. We report here a detailed structural and functional characterization of new variant Zn8:AB54, which houses similar, unsaturated Zn coordination sites to those in Zn8:(A104/G57)AB34, but in completely different microenvironments. Zn8:AB54 displays Michaelis-Menten behavior for ampicillin hydrolysis without any optimization. Yet, the subsequent directed evolution of Zn8:AB54 revealed limited catalytic improvement, which we ascribed to the local protein rigidity surrounding the Zn centers and the lack of evolvable loop structures nearby. The relaxation of local rigidity via the elimination of adjacent disulfide linkages led to a considerable structural transformation with a concomitant improvement in beta-lactamase activity. Our findings reaffirm previous observations that the delicate balance between protein flexibility and stability is crucial for enzyme design and evolution.
Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-beta-lactamases.,Song WJ, Yu J, Tezcan FA J Am Chem Soc. 2017 Nov 22;139(46):16772-16779. doi: 10.1021/jacs.7b08981. Epub, 2017 Nov 9. PMID:28992705[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Song WJ, Yu J, Tezcan FA. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-beta-lactamases. J Am Chem Soc. 2017 Nov 22;139(46):16772-16779. doi: 10.1021/jacs.7b08981. Epub, 2017 Nov 9. PMID:28992705 doi:http://dx.doi.org/10.1021/jacs.7b08981
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