7cgd: Difference between revisions
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<StructureSection load='7cgd' size='340' side='right'caption='[[7cgd]], [[Resolution|resolution]] 2.06Å' scene=''> | <StructureSection load='7cgd' size='340' side='right'caption='[[7cgd]], [[Resolution|resolution]] 2.06Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7cgd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[7cgd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CGD FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.06Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG:SILVER+ION'>AG</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=7cgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cgd OCA], [https://pdbe.org/7cgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cgd RCSB], [https://www.ebi.ac.uk/pdbsum/7cgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cgd 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=7cgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cgd OCA], [https://pdbe.org/7cgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cgd RCSB], [https://www.ebi.ac.uk/pdbsum/7cgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cgd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/MDH_ECOLI MDH_ECOLI] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516] | |||
<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 7cgd" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 7cgd" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Sun H]] | |||
[[Category: Sun | [[Category: Wang H]] | ||
[[Category: Wang | [[Category: Wang M]] | ||
[[Category: Wang | |||
Latest revision as of 19:07, 29 November 2023
Silver-bound E.coli malate dehydrogenaseSilver-bound E.coli malate dehydrogenase
Structural highlights
FunctionMDH_ECOLI Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516] Publication Abstract from PubMedUnderstanding how metallodrugs interact with their protein targets is of vital importance for uncovering their molecular mode of actions as well as overall pharmacological/toxicological profiles, which in turn facilitates the development of novel metallodrugs. Silver has been used as an antimicrobial agent since antiquity, yet there is limited knowledge about silver-binding proteins. Given the multiple dispersed cysteine residues and histidine-methionine pairs, Escherichia coli malate dehydrogenase (EcMDH) represents an excellent model to investigate silver coordination chemistry as well as its targeting sites in enzymes. We show by systematic biochemical characterizations that silver ions (Ag(+)) bind EcMDH at multiple sites including three cysteine-containing sites. By X-ray crystallography, we unravel the binding preference of Ag(+) to multiple binding sites in EcMDH, i.e., Cys113 > Cys251 > Cys109 > Met227. Silver exhibits preferences to the donor atoms and residues in the order of S > N > O and Cys > Met > His > Lys > Val, respectively, in EcMDH. For the first time, we report the coordination of silver to a lysine in proteins. Besides, we also observed argentophilic interactions (Agcdots, three dots, centeredAg, 2.7 to 3.3 A) between two silver ions coordinating to one thiolate. Combined with site-directed mutagenesis and an enzymatic activity test, we unveil that the binding of Ag(+) to the site IV (His177-Ag-Met227 site) plays a vital role in Ag(+)-mediated MDH inactivation. This work stands as the first unusual and explicit study of silver binding preference to multiple binding sites in its authentic protein target at the atomic resolution. These findings enrich our knowledge on the biocoordination chemistry of silver(i), which in turn facilitates the prediction of the unknown silver-binding proteins and extends the pharmaceutical potentials of metal-based drugs. Atomic differentiation of silver binding preference in protein targets: Escherichia coli malate dehydrogenase as a paradigm.,Wang H, Yang X, Wang M, Hu M, Xu X, Yan A, Hao Q, Li H, Sun H Chem Sci. 2020 Sep 10;11(43):11714-11719. doi: 10.1039/d0sc04151c. PMID:34123202[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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