4fr7: Difference between revisions

Revision as of 20:07, 19 October 2022

Crystal structure of the metallo-beta-lactamase VIM-31 in its reduced form at 1.61 A

Structural highlights

4fr7 is a 1 chain structure with sequence from Enterobacter cloacae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ACT, CL, OCS, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

I3RJZ3_ENTCL

Publication Abstract from PubMed

The metallo-beta-lactamase VIM-31 differs from VIM-2 by only two Tyr224His and His252Arg substitutions. Located close to the active site, the Tyr224His substitution is also present in VIM-1, VIM-4, VIM-7 and VIM-12. The VIM-31 variant was reported in 2012 from Enterobacter cloacae and kinetically characterized. It exhibits globally lower catalytic efficiencies than VIM-2. In the present study, we report the three-dimensional structures of VIM-31 in its native (reduced) and oxidized forms. The so-called 'flapping-loop' (loop 1) and loop 3 of VIM-31 were not positioned as in VIM-2 but instead were closer to the active site as in VIM-4, resulting in a narrower active site in VIM-31. Also, the presence of His224 in VIM-31 disrupts hydrogen-bonding networks close to the active site. Moreover, a third zinc-binding site, which also exists in VIM-2 structures, could be identified as a structural explanation for the decreased activity of VIM-MBLs at high zinc concentrations.

The three-dimensional structure of VIM-31 - a metallo-beta-lactamase from Enterobacter cloacae in its native and oxidized form.,Kupper MB, Herzog K, Bennink S, Schlomer P, Bogaerts P, Glupczynski Y, Fischer R, Bebrone C, Hoffmann KM FEBS J. 2015 Mar 30. doi: 10.1111/febs.13283. PMID:25825035^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kupper MB, Herzog K, Bennink S, Schlomer P, Bogaerts P, Glupczynski Y, Fischer R, Bebrone C, Hoffmann KM. The three-dimensional structure of VIM-31 - a metallo-beta-lactamase from Enterobacter cloacae in its native and oxidized form. FEBS J. 2015 Mar 30. doi: 10.1111/febs.13283. PMID:25825035 doi:https://dx.doi.org/10.1111/febs.13283

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OCA

[1] Kupper MB, Herzog K, Bennink S, Schlomer P, Bogaerts P, Glupczynski Y, Fischer R, Bebrone C, Hoffmann KM. The three-dimensional structure of VIM-31 - a metallo-beta-lactamase from Enterobacter cloacae in its native and oxidized form. FEBS J. 2015 Mar 30. doi: 10.1111/febs.13283. PMID:25825035 doi:https://dx.doi.org/10.1111/febs.13283

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the metallo-beta-lactamase VIM-31 in its reduced form at 1.61 A==
-<StructureSection load='4fr7' size='340' side='right' caption='[[4fr7]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
+<StructureSection load='4fr7' size='340' side='right'caption='[[4fr7]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fr7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FR7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fr7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FR7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=4fr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fr7 OCA], [https://pdbe.org/4fr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fr7 RCSB], [https://www.ebi.ac.uk/pdbsum/4fr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fr7 ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fsb|4fsb]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blaVIM-31 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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=4fr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fr7 OCA], [http://pdbe.org/4fr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fr7 RCSB], [http://www.ebi.ac.uk/pdbsum/4fr7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fr7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/I3RJZ3_ENTCL I3RJZ3_ENTCL]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 20: @@
 ==See Also==
-*[[Beta-lactamase|Beta-lactamase]]
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Herzog, K]]
+[[Category: Enterobacter cloacae]]
-[[Category: Hoffmann, K M]]
+[[Category: Large Structures]]
-[[Category: Beta-lactam hydrolyzing enzyme]]
+[[Category: Herzog K]]
-[[Category: Hydrolase]]
+[[Category: Hoffmann KM]]
-[[Category: Metallo-beta-lactamase superfamily]]
-[[Category: Zinc binding]]

4fr7: Difference between revisions

Revision as of 20:07, 19 October 2022

Crystal structure of the metallo-beta-lactamase VIM-31 in its reduced form at 1.61 A

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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