7bz3: Difference between revisions

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<StructureSection load='7bz3' size='340' side='right'caption='[[7bz3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='7bz3' size='340' side='right'caption='[[7bz3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7bz3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[7bz3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6j4n|6j4n]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=7bz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz3 OCA], [https://pdbe.org/7bz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz3 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz3 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=7bz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz3 OCA], [https://pdbe.org/7bz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz3 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz3 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A2U8UYM6_9BACT A0A2U8UYM6_9BACT]
The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although beta-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to beta-lactam antibiotics by producing beta-lactamases. Among beta-lactamases, metallo-beta-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes beta-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and beta-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.


Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants.,Park YS, Kim TY, Park H, Lee JH, Nguyen DQ, Hong MK, Lee SH, Kang LW Int J Mol Sci. 2020 Jul 12;21(14). pii: ijms21144926. doi: 10.3390/ijms21144926. PMID:32664695<ref>PMID:32664695</ref>
==See Also==
 
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7bz3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Beta-lactamase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Kang, L W]]
[[Category: Uncultured bacterium]]
[[Category: Lee, J H]]
[[Category: Kang LW]]
[[Category: Park, Y S]]
[[Category: Lee JH]]
[[Category: Antibiotic]]
[[Category: Park YS]]
[[Category: Carbapenemase]]
[[Category: Mbl]]
[[Category: Rnase z]]

Latest revision as of 10:49, 27 March 2024

The mutant variant of PNGM-1. H257 was substituted for alanine to study substrate binding.

7bz3, resolution 2.00Å

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