6jki: Difference between revisions
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The | ==Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa== | ||
<StructureSection load='6jki' size='340' side='right'caption='[[6jki]], [[Resolution|resolution]] 2.59Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6jki]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_UCBPP-PA14 Pseudomonas aeruginosa UCBPP-PA14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JKI FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.59Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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=6jki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jki OCA], [https://pdbe.org/6jki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jki RCSB], [https://www.ebi.ac.uk/pdbsum/6jki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jki ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TRMD_PSEAE TRMD_PSEAE] Specifically methylates guanosine-37 in various tRNAs. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The tRNA (m(1)G37) methyltransferase TrmD catalyzes m(1)G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial role, little is known about TrmD in Pseudomonas aeruginosa (PaTrmD), an important human pathogen. Here we present detailed structural, substrate and kinetic properties of PaTrmD. Mass spectrometric analysis confirmed the G36G37-containing tRNAs Leu(GAG), Leu(CAG), Leu(UAG), Pro(GGG), Pro(UGG), Pro(CGG), and His(GUG) as PaTrmD substrates. Analysis of steady-state kinetics with S-adenosyl-L-methionine (SAM) and tRNA(Leu(GAG)) showed that PaTrmD catalyzes the two-substrate reaction by way of a ternary-complex, while isothermal titration calorimetry revealed that SAM and tRNA(Leu(GAG)) bind to PaTrmD independently, each with a dissociation constant of 14 +/- 3 microM. Inhibition by the SAM analog sinefungin was competitive with respect to SAM (Ki = 0.41 +/- 0.07 microM) and uncompetitive for tRNA (Ki = 6.4 +/- 0.8 microM). A set of crystal structures of the homodimeric PaTrmD protein bound to SAM and sinefungin provide the molecular basis for enzyme competitive inhibition and identify the location of the bound divalent ion. These results provide insights into PaTrmD as a potential target for the development of antibiotics. | |||
Crystal structure and catalytic mechanism of the essential m(1)G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa.,Jaroensuk J, Wong YH, Zhong W, Liew CW, Maenpuen S, Sahili AE, Atichartpongkul S, Chionh YH, Nah Q, Thongdee N, McBee ME, Prestwich EG, DeMott MS, Chaiyen P, Mongkolsuk S, Dedon P, Lescar J, Fuangthong M RNA. 2019 Aug 9. pii: rna.066746.118. doi: 10.1261/rna.066746.118. PMID:31399541<ref>PMID:31399541</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6jki" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Chionh | ==See Also== | ||
[[Category: | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pseudomonas aeruginosa UCBPP-PA14]] | ||
[[Category: | [[Category: Atichartpongkul S]] | ||
[[Category: | [[Category: Chionh YH]] | ||
[[Category: | [[Category: DeMott MS]] | ||
[[Category: | [[Category: Dedon PC]] | ||
[[Category: Fuangthong M]] | |||
[[Category: Jaroensuk J]] | |||
[[Category: Lescar J]] | |||
[[Category: Liew CW]] | |||
[[Category: McBee ME]] | |||
[[Category: Mongkolsuk S]] | |||
[[Category: Prestwich EG]] | |||
[[Category: Thongdee N]] | |||
[[Category: Wong YH]] | |||
[[Category: Zhong WH]] | |||
Latest revision as of 13:13, 22 November 2023
Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosaCrystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa
Structural highlights
FunctionTRMD_PSEAE Specifically methylates guanosine-37 in various tRNAs. Publication Abstract from PubMedThe tRNA (m(1)G37) methyltransferase TrmD catalyzes m(1)G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial role, little is known about TrmD in Pseudomonas aeruginosa (PaTrmD), an important human pathogen. Here we present detailed structural, substrate and kinetic properties of PaTrmD. Mass spectrometric analysis confirmed the G36G37-containing tRNAs Leu(GAG), Leu(CAG), Leu(UAG), Pro(GGG), Pro(UGG), Pro(CGG), and His(GUG) as PaTrmD substrates. Analysis of steady-state kinetics with S-adenosyl-L-methionine (SAM) and tRNA(Leu(GAG)) showed that PaTrmD catalyzes the two-substrate reaction by way of a ternary-complex, while isothermal titration calorimetry revealed that SAM and tRNA(Leu(GAG)) bind to PaTrmD independently, each with a dissociation constant of 14 +/- 3 microM. Inhibition by the SAM analog sinefungin was competitive with respect to SAM (Ki = 0.41 +/- 0.07 microM) and uncompetitive for tRNA (Ki = 6.4 +/- 0.8 microM). A set of crystal structures of the homodimeric PaTrmD protein bound to SAM and sinefungin provide the molecular basis for enzyme competitive inhibition and identify the location of the bound divalent ion. These results provide insights into PaTrmD as a potential target for the development of antibiotics. Crystal structure and catalytic mechanism of the essential m(1)G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa.,Jaroensuk J, Wong YH, Zhong W, Liew CW, Maenpuen S, Sahili AE, Atichartpongkul S, Chionh YH, Nah Q, Thongdee N, McBee ME, Prestwich EG, DeMott MS, Chaiyen P, Mongkolsuk S, Dedon P, Lescar J, Fuangthong M RNA. 2019 Aug 9. pii: rna.066746.118. doi: 10.1261/rna.066746.118. PMID:31399541[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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