3l6n: Difference between revisions
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==Crystal structure of metallo-beta-lactamase IND-7== | ==Crystal structure of metallo-beta-lactamase IND-7== | ||
<StructureSection load='3l6n' size='340' side='right' caption='[[3l6n]], [[Resolution|resolution]] 1.65Å' scene=''> | <StructureSection load='3l6n' size='340' side='right'caption='[[3l6n]], [[Resolution|resolution]] 1.65Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3l6n]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3l6n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chryseobacterium_indologenes Chryseobacterium indologenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L6N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L6N 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]] 1.65Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3l6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6n OCA], [https://pdbe.org/3l6n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l6n RCSB], [https://www.ebi.ac.uk/pdbsum/3l6n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6n ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A4GRB2_9FLAO A4GRB2_9FLAO] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/3l6n_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/3l6n_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3l6n ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3l6n" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Beta-lactamase|Beta-lactamase]] | *[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Chryseobacterium indologenes]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Kurosaki | [[Category: Kurosaki H]] | ||
[[Category: Yamagata | [[Category: Yamagata Y]] | ||
[[Category: Yamaguchi | [[Category: Yamaguchi Y]] | ||
Latest revision as of 19:21, 1 November 2023
Crystal structure of metallo-beta-lactamase IND-7Crystal structure of metallo-beta-lactamase IND-7
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe X-ray crystal structure of metallo-beta-lactamase from Chryseobacterium indologenes IND-7 was determined at a resolution of 1.65 A. The overall structure adopted a four-layered alphabeta/betaalpha sandwich structure with a dinuclear zinc(II) active site, in which the zinc(II) ions were denoted as Zn1 and Zn2. The overall structure of IND-7 is analogous to those of subclass B1 metallo-beta-lactamases, as determined by X-ray crystallography. A significant structural difference, however, was observed in the dinuclear zinc(II) active site: the coordination geometry around Zn1 changed from tetrahedral, found in other subclass B1 metallo-beta-lactamases, to distorted trigonal bipyramidal, whereas that of Zn2 changed from trigonal bipyramidal to tetrahedral. Arg121(101), which is located in the vicinity of the dinuclear zinc(II) active site, may affect the binding affinity of Zn2 due to an electronic repulsion between the zinc(II) ion(s) and a positively charged guanidyl group of Arg121(101). Moreover, the hydrogen-bonding interaction of Arg121 with Ser71(53), which is conserved in IND-1, IND-3 and IND-5-IND-7, appeared to have important consequences for the binding affinity of Zn2 in conjunction with the above electrostatic effect. Structure of metallo-beta-lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution.,Yamaguchi Y, Takashio N, Wachino J, Yamagata Y, Arakawa Y, Matsuda K, Kurosaki H J Biochem. 2010 Jun;147(6):905-15. Epub 2010 Mar 19. PMID:20305272[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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