2wfg

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct

Structural highlights

2wfg is a 1 chain structure with sequence from Candida albicans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Leucyl-tRNA synthetase (LeuRS) specifically links leucine to the 3' end of tRNA(leu) isoacceptors. The overall accuracy of the two-step aminoacylation reaction is enhanced by an editing domain that hydrolyzes mischarged tRNAs, notably ile-tRNA(leu). We present crystal structures of the editing domain from two eukaryotic cytosolic LeuRS: human and fungal pathogen Candida albicans. In comparison with previous structures of the editing domain from bacterial and archeal kingdoms, these structures show that the LeuRS editing domain has a conserved structural core containing the active site for hydrolysis, with distinct bacterial, archeal, or eukaryotic specific peripheral insertions. It was recently shown that the benzoxaborole antifungal compound AN2690 (5-fluoro-1,3-dihydro-1-hydroxy-1,2-benzoxaborole) inhibits LeuRS by forming a covalent adduct with the 3' adenosine of tRNA(leu) at the editing site, thus locking the enzyme in an inactive conformation. To provide a structural basis for enhancing the specificity of these benzoxaborole antifungals, we determined the structure at 2.2 A resolution of the C. albicans editing domain in complex with a related compound, AN3018 (6-(ethylamino)-5-fluorobenzo[c][1,2]oxaborol-1(3H)-ol), using AMP as a surrogate for the 3' adenosine of tRNA(leu). The interactions between the AN3018-AMP adduct and C. albicans LeuRS are similar to those previously observed for bacterial LeuRS with the AN2690 adduct, with an additional hydrogen bond to the extra ethylamine group. However, compared to bacteria, eukaryotic cytosolic LeuRS editing domains contain an extra helix that closes over the active site, largely burying the adduct and providing additional direct and water-mediated contacts. Small differences between the human domain and the fungal domain could be exploited to enhance fungal specificity.

Crystal structures of the human and fungal cytosolic Leucyl-tRNA synthetase editing domains: A structural basis for the rational design of antifungal benzoxaboroles.,Seiradake E, Mao W, Hernandez V, Baker SJ, Plattner JJ, Alley MR, Cusack S J Mol Biol. 2009 Jul 10;390(2):196-207. Epub 2009 May 6. PMID:19426743^[1]

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

References

↑ Seiradake E, Mao W, Hernandez V, Baker SJ, Plattner JJ, Alley MR, Cusack S. Crystal structures of the human and fungal cytosolic Leucyl-tRNA synthetase editing domains: A structural basis for the rational design of antifungal benzoxaboroles. J Mol Biol. 2009 Jul 10;390(2):196-207. Epub 2009 May 6. PMID:19426743 doi:10.1016/j.jmb.2009.04.073

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wfg"

@@ Line 1: / Line 1: @@
-==STRUCTURE OF THE CANDIDA ALBICANS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN BOUND TO A BENZOXABOROLE-AMP ADDUCT==
+==Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct==
-<StructureSection load='2wfg' size='340' side='right' caption='[[2wfg]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='2wfg' size='340' side='right'caption='[[2wfg]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[candida_stellatoidea]] Atcc 11006 [[candida stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WFG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wfg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WFG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZZB:[(1S,3S,5R,6R,8R)-6-(6-AMINOPURIN-9-YL)-4-ETHYLAMINO-3-FLUORO-SPIRO[2,4,7-TRIOXA-3-BORANUIDABICYCLO[3.3.0]OCTANE-3,7-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIENE]-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>ZZB</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wfe|2wfe]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZZB:[(1S,3S,5R,6R,8R)-6-(6-AMINOPURIN-9-YL)-4-ETHYLAMINO-3-FLUORO-SPIRO[2,4,7-TRIOXA-3-BORANUIDABICYCLO[3.3.0]OCTANE-3,7-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIENE]-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>ZZB</scene></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=2wfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wfg OCA], [http://pdbe.org/2wfg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2wfg RCSB], [http://www.ebi.ac.uk/pdbsum/2wfg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2wfg 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=2wfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wfg OCA], [https://pdbe.org/2wfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wfg RCSB], [https://www.ebi.ac.uk/pdbsum/2wfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wfg ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 12: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wf/2wfg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wf/2wfg_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Alley, M R.K]]
+[[Category: Candida albicans]]
-[[Category: Baker, S J]]
+[[Category: Large Structures]]
-[[Category: Cusack, S]]
+[[Category: Alley MRK]]
-[[Category: Hernandez, V]]
+[[Category: Baker SJ]]
-[[Category: Mao, W]]
+[[Category: Cusack S]]
-[[Category: Plattner, J J]]
+[[Category: Hernandez V]]
-[[Category: Seiradake, E]]
+[[Category: Mao W]]
-[[Category: Anti-fungal]]
+[[Category: Plattner JJ]]
-[[Category: Benzoxaborole]]
+[[Category: Seiradake E]]
-[[Category: Candida albican]]
-[[Category: Editing domain]]
-[[Category: Hydrolysis of mis-charged trna]]
-[[Category: Leucyl-trna synthetase]]
-[[Category: Ligase]]

2wfg

From Proteopedia

Current revision

Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox