4ua6: Difference between revisions
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''' | ==CTX-M-14 Class A Beta-Lactamase Apo Crystal Structure at 0.79 Angstrom Resolution== | ||
<StructureSection load='4ua6' size='340' side='right' caption='[[4ua6]], [[Resolution|resolution]] 0.79Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ua6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UA6 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ua7|4ua7]], [[4ua9|4ua9]], [[4uaa|4uaa]]</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=4ua6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ua6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ua6 RCSB], [http://www.ebi.ac.uk/pdbsum/4ua6 PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ligand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M beta-lactamase, directly visualizing protonation state changes along the enzymatic pathway: apo protein at 0.79 A, precovalent complex with nonelectrophilic ligand at 0.89 A, and acylation transition state (TS) analogue at 0.84 A. Binding of the noncovalent ligand induces a proton transfer from the catalytic Ser70 to the negatively charged Glu166, and the formation of a low-barrier hydrogen bond (LBHB) between Ser70 and Lys73, with a length of 2.53 A and the shared hydrogen equidistant from the heteroatoms. QM/MM reaction path calculations determined the proton transfer barrier to be 1.53 kcal/mol. The LBHB is absent in the other two structures although Glu166 remains neutral in the covalent complex. Our data represents the first X-ray crystallographic example of a hydrogen engaged in an enzymatic LBHB, and demonstrates that desolvation of the active site by ligand binding can provide a protein microenvironment conducive to LBHB formation. It also suggests that LBHBs may contribute to stabilization of the TS in general acid/base catalysis together with other preorganized features of enzyme active sites. These structures reconcile previous experimental results suggesting alternatively Glu166 or Lys73 as the general base for acylation, and underline the importance of considering residue protonation state change when modeling protein-ligand interactions. Additionally, the observation of another LBHB (2.47 A) between two conserved residues, Asp233 and Asp246, suggests that LBHBs may potentially play a special structural role in proteins. | |||
Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography.,Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith EW, Wang KK, Prati F, Renslo AR, Woodcock HL, Chen Y J Am Chem Soc. 2015 Jun 22. PMID:26057252<ref>PMID:26057252</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Chen, Y]] | [[Category: Chen, Y]] | ||
[[Category: Nichols, D | [[Category: Nichols, D A]] | ||
[[Category: Apo]] | |||
[[Category: Class a beta-lactamase]] | |||
[[Category: Ctx-m-14]] | |||
[[Category: Hydrolase]] | |||
[[Category: Ultra high resolution]] | |||
Revision as of 15:53, 24 June 2015
CTX-M-14 Class A Beta-Lactamase Apo Crystal Structure at 0.79 Angstrom ResolutionCTX-M-14 Class A Beta-Lactamase Apo Crystal Structure at 0.79 Angstrom Resolution
Structural highlights
Publication Abstract from PubMedLigand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M beta-lactamase, directly visualizing protonation state changes along the enzymatic pathway: apo protein at 0.79 A, precovalent complex with nonelectrophilic ligand at 0.89 A, and acylation transition state (TS) analogue at 0.84 A. Binding of the noncovalent ligand induces a proton transfer from the catalytic Ser70 to the negatively charged Glu166, and the formation of a low-barrier hydrogen bond (LBHB) between Ser70 and Lys73, with a length of 2.53 A and the shared hydrogen equidistant from the heteroatoms. QM/MM reaction path calculations determined the proton transfer barrier to be 1.53 kcal/mol. The LBHB is absent in the other two structures although Glu166 remains neutral in the covalent complex. Our data represents the first X-ray crystallographic example of a hydrogen engaged in an enzymatic LBHB, and demonstrates that desolvation of the active site by ligand binding can provide a protein microenvironment conducive to LBHB formation. It also suggests that LBHBs may contribute to stabilization of the TS in general acid/base catalysis together with other preorganized features of enzyme active sites. These structures reconcile previous experimental results suggesting alternatively Glu166 or Lys73 as the general base for acylation, and underline the importance of considering residue protonation state change when modeling protein-ligand interactions. Additionally, the observation of another LBHB (2.47 A) between two conserved residues, Asp233 and Asp246, suggests that LBHBs may potentially play a special structural role in proteins. Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography.,Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith EW, Wang KK, Prati F, Renslo AR, Woodcock HL, Chen Y J Am Chem Soc. 2015 Jun 22. PMID:26057252[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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