2jje: Difference between revisions

Latest revision as of 08:28, 9 April 2025

Crystal structure of T330S mutant of Rv3290c from M. tuberculosis

Structural highlights

2jje is a 1 chain structure with sequence from Mycobacterium tuberculosis. 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:	PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LAT_MYCTU

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

Lysine varepsilon-aminotransferase (LAT) converts lysine to alpha-aminoadipate-delta-semialdehyde in a PLP-mediated reaction. We mutated active-site T330, N328 and E243, and structurally rationalized their properties. T330A and T330S mutants cannot bind PLP and are inactive. N328A although inactive, binds to PLP. E243A retains activity, but binds alpha-ketoglutarate in a different conformation. We had earlier identified 2-aminomethyl piperidine derivative as a LAT inhibitor. The co-crystal structure reveals that it mimics binding of C5 substrates and exhibits two binding modes. E243, that shields R422 in the apo enzyme, exhibits conformational changes to permit the binding of the inhibitor in one of the binding modes. Structure-based analysis of bound water in the active site suggests optimization strategies for synthesis of improved inhibitors.

Mutational analysis of Mycobacterium tuberculosis lysine varepsilon-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes.,Tripathi SM, Agarwal A, Ramachandran R Biochem Biophys Res Commun. 2015 Jul 17-24;463(1-2):154-60. doi:, 10.1016/j.bbrc.2015.05.055. Epub 2015 May 20. PMID:26003725^[1]

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

References

↑ Tripathi SM, Agarwal A, Ramachandran R. Mutational analysis of Mycobacterium tuberculosis lysine varepsilon-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes. Biochem Biophys Res Commun. 2015 Jul 17-24;463(1-2):154-60. doi:, 10.1016/j.bbrc.2015.05.055. Epub 2015 May 20. PMID:26003725 doi:https://dx.doi.org/10.1016/j.bbrc.2015.05.055

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tripathi SM, Agarwal A, Ramachandran R. Mutational analysis of Mycobacterium tuberculosis lysine varepsilon-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes. Biochem Biophys Res Commun. 2015 Jul 17-24;463(1-2):154-60. doi:, 10.1016/j.bbrc.2015.05.055. Epub 2015 May 20. PMID:26003725 doi:https://dx.doi.org/10.1016/j.bbrc.2015.05.055

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='2jje' size='340' side='right'caption='[[2jje]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jje]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JJE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2JJE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jje]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JJE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JJE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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">[[2jjf|2jjf]], [[2jjg|2jjg]], [[2jjh|2jjh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lysine_6-transaminase L-lysine 6-transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.36 2.6.1.36] </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=2jje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jje OCA], [https://pdbe.org/2jje PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jje RCSB], [https://www.ebi.ac.uk/pdbsum/2jje PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jje ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2jje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jje OCA], [http://pdbe.org/2jje PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jje RCSB], [http://www.ebi.ac.uk/pdbsum/2jje PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jje ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LAT_MYCTU LAT_MYCTU]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jj/2jje_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: L-lysine 6-transaminase]]
 [[Category: Large Structures]]
-[[Category: Ramachandran, R]]
-[[Category: Tripathi, S M]]
-[[Category: Aminotransferase]]
-[[Category: Lysine amino transferase]]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Plp]]
+[[Category: Ramachandran R]]
-[[Category: Pyridoxal phosphate]]
+[[Category: Tripathi SM]]
-[[Category: Rv3290c]]
-[[Category: T330s mutant]]
-[[Category: Transferase]]

2jje: Difference between revisions

Latest revision as of 08:28, 9 April 2025

Crystal structure of T330S mutant of Rv3290c from M. tuberculosis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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