Flexibility and communication within the structure of the <i>Mycobacterium smegmatis</i> methionyl‐tRNA synthetase

Ingvarsson, Henrik; Unge, Torsten

doi:10.1111/j.1742-4658.2010.07784.x

Cited by 14 publications

(13 citation statements)

References 46 publications

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“…The Met binding pockets of Tb MetRS in the two subunits are essentially the same and the protein adopts a conformation as observed in other MetRS structures in complex with Met (Ingvarsson and Unge, 2010; Serre et al, 2001) (Figure S4 and Table S1). …”

Section: Resultssupporting

confidence: 59%

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

et al. 2012

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Summary To guide development of new drugs targeting methionyl-tRNA synthetase (MetRS) for treatment of human African trypanosomiasis, crystal structure determinations of Trypanosoma brucei MetRS in complex with its substrate methionine and its intermediate product methionyl-adenylate were followed by those of the enzyme in complex with high-affinity aminoquinolone inhibitors via soaking experiments. Drastic changes in conformation of one of the two enzymes in the asymmetric unit allowed these inhibitors to occupy an enlarged methionine pocket and a new so-called auxiliary pocket. Interestingly, a small low-affinity compound caused the same conformational changes, removed the methionine without occupying the methionine pocket, and occupied the previously not existing auxiliary pocket. Analysis of these structures indicates that the binding of the inhibitors is the result of conformational selection, not induced fit.

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Section: Resultssupporting

confidence: 59%

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

et al. 2012

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“…The CP comprises two subdomains: subdomain CP1 formed by the antiparallel -strands 4 and 8, and subdomain CP2 formed by helices 5 and 6. Subdomain CP1 in MtubMetRS is in the closed conformation, as seen previously in the structure of MsmeMetRS and other MetRS structures (Ingvarsson & Unge, 2010). CP1 harbors one 'knuckle' devoid of residues able to coordinate Zn 2+ , which identifies MtubMetRS as a member of the MetRS1 form Green et al, 2009).…”

Section: Resultssupporting

confidence: 56%

“…Interestingly, when superimposing the MtubMetRS structure with the structure of the homologous M. smegmatis MetRS (Msme-MetRS), which shares 76% sequence identity overall and 94% identity in the Met-AMP-binding site, the KMSKS loop adopts dramatically different conformations in these two closely related tRNA synthetases. The KMSKS loop in MsmeMetRS, in the presence of either methionine (PDB entry 2x1m; Ingvarsson & Unge, 2010) or of methionine and adenosine (PDB entry 2x1l; Ingvarsson & Unge, 2010), is in a wide-open conformation (Fig. 2).…”

Section: Resultsmentioning

confidence: 99%

“…HKL-2000 (Otwinowski & Minor, 1997) was used for data processing. The structure of M. smegmatis MetRS (Ingvarsson & Unge, 2010; PDB entry 2x1l) was used as a model to obtain initial phases by molecular replacement using Phaser (McCoy et al, 2007). Iterations of manual building and rebuilding using Coot (Emsley et al, 2010) were alternated with refinement of the structure with REFMAC5 (Murshudov et al, 2011).…”

Section: Data Collection and Structure Determinationmentioning

confidence: 99%

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The crystal structure of the drug targetMycobacterium tuberculosismethionyl-tRNA synthetase in complex with a catalytic intermediate

Barros-Álvarez¹,

Turley²,

Ranade³

et al. 2018

Acta Cryst Sect F

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Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance. New treatment options are therefore urgently needed. Here, the crystal structure of methionyl-tRNA synthetase (MetRS), an enzyme critical for protein biosynthesis and therefore a drug target, in complex with its catalytic intermediate methionyl adenylate is reported. Phenylalanine 292 of the M. tuberculosis enzyme is in an `out' conformation and barely contacts the adenine ring, in contrast to other MetRS structures where ring stacking occurs between the adenine and a protein side-chain ring in the `in' conformation. A comparison with human cytosolic MetRS reveals substantial differences in the active site as well as regarding the position of the connective peptide subdomain 1 (CP1) near the active site, which bodes well for arriving at selective inhibitors. Comparison with the human mitochondrial enzyme at the amino-acid sequence level suggests that arriving at inhibitors with higher affinity for the mycobacterial enzyme than for the mitochondrial enzyme might be achievable.

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“…These include EcMetRS in apo form [58], in complex with methionine [57] and with intermediate product analogs [53], apo Pyrococcus abyssi MetRS [59], apo Thermus thermophilus MetRS [60], the binary complex of Aquifex aeolicus MetRS with tRNA Met and its ternary complex with 5’- O -[ N -(L-methionyl)-sulfamoyl] adenosine (MetSA) and tRNA Met [40], and most recently that of Mycobacterium smegmatis MetRS in complex with Met and with both Met and adenosine [61] (Supplementary Table 1). A comparison of these structures (Fig.…”

Section: Resultsmentioning

confidence: 99%

Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate

et al. 2011

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Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg 2+ ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of E. coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNA Met complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP-and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme.

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Flexibility and communication within the structure of the Mycobacterium smegmatis methionyl‐tRNA synthetase

Cited by 14 publications

References 46 publications

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

The crystal structure of the drug targetMycobacterium tuberculosismethionyl-tRNA synthetase in complex with a catalytic intermediate

Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate

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