Crystal Structure of Bacillus anthracis ThiI, a tRNA-modifying Enzyme Containing the Predicted RNA-binding THUMP Domain

Ortiz-Lombardı́a, M.; Fogg, Mark J.; Koonin, Eugene V.; Antson, A.A.

doi:10.1016/j.jmb.2005.11.013

Cited by 66 publications

(100 citation statements)

References 62 publications

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“…S2A). In addition, Cys 268 is adjacent to a highly conserved Lys or Arg residue (Arg 265 of B. anthracis ThiI), which is in contact with the phosphate group of AMP (24). Therefore, these two catalytic cysteines are presumably located near the adenylated form of U8.…”

Section: Proposed Model Of S 4 U Formation In M Maripaludis-mentioning

confidence: 99%

Biosynthesis of 4-Thiouridine in tRNA in the Methanogenic Archaeon Methanococcus maripaludis

Liu

Zhu

Nakamura

et al. 2012

Journal of Biological Chemistry

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Background: Bacterial ThiI catalyzes 4-thiouridine biosynthesis by using a rhodanese-like domain for sulfur transfer. Results: ThiI in methanogenic archaea employs a conserved CXXC motif to generate persulfide and disulfide intermediates for sulfur transfer. Conclusion: Methanogens possess a unique sulfur relay strategy. Significance: Sulfur metabolism in methanogens is a model for the evolution of sulfur metabolism in the anaerobic sulfide-rich environments common on ancient earth.

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Section: Proposed Model Of S 4 U Formation In M Maripaludis-mentioning

confidence: 99%

Biosynthesis of 4-Thiouridine in tRNA in the Methanogenic Archaeon Methanococcus maripaludis

Liu

Zhu

Nakamura

et al. 2012

Journal of Biological Chemistry

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“…These proteins have substrate specificity, recognizing uridine in the context of RNA, utilizing the sequence or structural context of their Adopts an a/b-fold similar to the C-terminus of translation initiation factor 3 [21,22] target site. Only the TruB family has a C-terminal PUA domain.…”

Section: Introductionmentioning

confidence: 99%

Protein universe containing a PUA RNA‐binding domain

2013

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Here, we review current knowledge about pseudouridine synthase and archaeosine transglycosylase (PUA)‐domain‐containing proteins to illustrate progress in this field. A methodological analysis of the literature about the topic was carried out, together with a ‘qualitative comparative analysis’ to give a more comprehensive review. Bioinformatics methods for whole‐protein or protein‐domain identification are commonly based on pairwise protein sequence comparisons; we added comparison of structures to detect the whole universe of proteins containing the PUA domain. We present an update of proteins having this domain, focusing on the specific proteins present in Homo sapiens (dyskerin, MCT1, Nip7, eIF2D and Nsun6), and explore the existence of these in other species. We also analyze the phylogenetic distribution of the PUA domain in different species and proteins. Finally, we performed a structural comparison of the PUA domain through data mining of structural databases, determining a conserved structural motif, despite the differences in the sequence, even among eukaryotes, archaea and bacteria. All data discussed in this review, both bibliographic and analytical, corroborate the functional importance of the PUA domain in RNA‐binding proteins.

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“…rearrangement, such as base flipping in the substrate tRNA, must occur to expose the target nucleoside and place it in the active site. The crystal structure of ThiI from B. anthracis showed that CTD contains the catalytic core (Waterman et al 2006). The conformational change detected on CD spectra may correspond to these rearrangements, i.e., base flipping of U8.…”

Section: Structural Changes In Rna Over Binding With Thiimentioning

confidence: 99%

“…ThiI from g-proteobacteria and archaea consists of four domains, i.e., an N-terminal ferredoxin-like domain (NFLD), thio uridine synthases RNA methyltransferases and pseudouridine synthases (THUMP), modified P-loop motif involved in pyrophosphate binding (PP-loop domain), and rhodanese-like domain (RLD) (Webb et al 1997;Palenchar et al 2000;Waterman et al 2006). As the THUMP domain is common to several RNA binding proteins, it likely acts as an RNA recognition motif (Aravind and Koonin 2001;Gabant et al 2006).…”

Section: Introductionmentioning

confidence: 99%

“…As the THUMP domain is common to several RNA binding proteins, it likely acts as an RNA recognition motif (Aravind and Koonin 2001;Gabant et al 2006). The crystal structures of ThiI from Pyrococcus horikoshii and Bacillus anthracis, which did not contain RLD, revealed an elongated structure in which the THUMP domain and the PP-loop domain were separated, with NFLD located between them (Waterman et al 2006). As AMP was found in the PP-loop domain of B. anthracis ThiI, the PP-loop domain was thought to be an active domain.…”

Section: Introductionmentioning

confidence: 99%

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Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand

Tanaka

Yamagata

Kitago

et al. 2009

RNA

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ThiI catalyzes the thio-introduction reaction to tRNA, and a truncated tRNA consisting of 39 nucleotides, TPHE39A, is the minimal RNA substrate for modification by ThiI from Escherichia coli. To examine the molecular basis of the tRNA recognition by ThiI, we have solved the crystal structure of TPHE39A, which showed that base pairs in the T-stem were almost completely disrupted, although those in the acceptor-stem were preserved. Gel shift assays and isothermal titration calorimetry experiments showed that ThiI can efficiently bind with not only tRNA Phe but also TPHE39A. Binding assays using truncated ThiI, i.e., N-and C-terminal domains of ThiI, showed that the N-domain can bind with both tRNA Phe and TPHE39A, whereas the C-domain cannot. These results indicated that the N-domain of ThiI recognizes the acceptor-stem region. Thermodynamic analysis indicated that the C-domain also affects RNA binding by its enthalpically favorable, but entropically unfavorable, contribution. In addition, circular dichroism spectra showed that the C-domain induced a conformation change in tRNA Phe . Based on these results, a possible RNA binding mechanism of ThiI in which the N-terminal domain recognizes the acceptor-stem region and the C-terminal region causes a conformational change of RNA is proposed.

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Crystal Structure of Bacillus anthracis ThiI, a tRNA-modifying Enzyme Containing the Predicted RNA-binding THUMP Domain

Cited by 66 publications

References 62 publications

Biosynthesis of 4-Thiouridine in tRNA in the Methanogenic Archaeon Methanococcus maripaludis

Biosynthesis of 4-Thiouridine in tRNA in the Methanogenic Archaeon Methanococcus maripaludis

Protein universe containing a PUA RNA‐binding domain

Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand

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