Crystal structure of the YciO protein from <i>Escherichia coli</i>

Jia, Jia; Лунин, В.В.; Sauvé, Véronique; Huang, L.; Matte, Allan; Cygler, Mirosław

doi:10.1002/prot.10178

Cited by 21 publications

(10 citation statements)

References 13 publications

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“…For several more proteins, such as HI0065 (YjeE, COG0802), HI0315 (YebC, COG0217), HI0656 (YciO, COG0009), and HI0719 (YjgF, COG0251), the exact functions remain unknown even though the crystal structures have been resolved in structural genomics studies (28,62) and the predicted biochemical functions have been listed in the database (57). Our observation that these proteins are detected either under both growth conditions (HI0719) or predominantly during microaerobic growth (HI0065, HI0315, HI0656) might eventually help in pinpointing their functions.…”

Section: Conserved Hypothetical Proteinsmentioning

confidence: 99%

Initial Proteome Analysis of Model MicroorganismHaemophilus influenzaeStrain Rd KW20

Kolker¹,

Purvine²,

Galperin

et al. 2003

J Bacteriol

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The proteome of Haemophilus influenzae strain Rd KW20 was analyzed by liquid chromatography (LC) coupled with ion trap tandem mass spectrometry (MS/MS). This approach does not require a gel electrophoresis step and provides a rapidly developed snapshot of the proteome. In order to gain insight into the central metabolism of H. influenzae, cells were grown microaerobically and anaerobically in a rich medium and soluble and membrane proteins of strain Rd KW20 were proteolyzed with trypsin and directly examined by LC-MS/MS. Several different experimental and computational approaches were utilized to optimize the proteome coverage and to ensure statistically valid protein identification. Approximately 25% of all predicted proteins (open reading frames) of H. influenzae strain Rd KW20 were identified with high confidence, as their component peptides were unambiguously assigned to tandem mass spectra. Approximately 80% of the predicted ribosomal proteins were identified with high confidence, compared to the 33% of the predicted ribosomal proteins detected by previous two-dimensional gel electrophoresis studies. The results obtained in this study are generally consistent with those obtained from computational genome analysis, two-dimensional gel electrophoresis, and whole-genome transposon mutagenesis studies. At least 15 genes originally annotated as conserved hypothetical were found to encode expressed proteins. Two more proteins, previously annotated as predicted coding regions, were detected with high confidence; these proteins also have close homologs in related bacteria. The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism.

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Section: Conserved Hypothetical Proteinsmentioning

confidence: 99%

Initial Proteome Analysis of Model MicroorganismHaemophilus influenzaeStrain Rd KW20

Kolker¹,

Purvine²,

Galperin

et al. 2003

J Bacteriol

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“…E. coli YrdC contains a novel fold with a heavily twisted central β‐sheet, which forms a basic concave surface that may preferentially bind double‐stranded RNAs 43. This fold is shared by YciO 45. The structure of S. tokodaii Sua5 revealed that the N‐terminal YrdC domain contains an E. coli ‐derived AMP molecule, and its ATP hydrolysis activity in the presence of Mg 2+ was confirmed 44.…”

Section: Introductionmentioning

confidence: 98%

Crystal structure of sulfolobus tokodaii sua5 complexed with L‐threonine and AMPPNP

et al. 2011

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The hypermodified nucleoside N(6)-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N(6)-threonylcarbamoyl moiety is composed of L-threonine and bicarbonate, and its synthesis was genetically shown to require YrdC/Sua5. YrdC/Sua5 binds to tRNA and ATP. In this study, we analyzed the L-threonine-binding mode of Sua5 from the archaeon Sulfolobus tokodaii. Isothermal titration calorimetry measurements revealed that S. tokodaii Sua5 binds L-threonine more strongly than L-serine and glycine. The Kd values of Sua5 for L-threonine and L-serine are 9.3 μM and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L-threonine, at 1.8 Å resolution. The L-threonine is bound next to AMPPNP in the same pocket of the N-terminal domain. Thr118 and two water molecules form hydrogen bonds with AMPPNP in a unique manner for adenine-specific recognition. The carboxyl group and the side-chain hydroxyl and methyl groups of L-threonine are buried deep in the pocket, whereas the amino group faces AMPPNP. The L-threonine is located in a suitable position to react together with ATP for the synthesis of N(6)-threonylcarbamoyladenosine.

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“…The crystal structures of two Escherichia coli COG0009 family members YrdC and YciO (2,3) reveal an α/β twisted open-sheet structure with a positively charged cleft in its center that was proposed to form a nucleic-acid-binding site (2). Binding to double-stranded RNA (including tRNA) was experimentally verified for the E. coli YrdC protein (YrdC Ec ) (2).…”

Section: Introductionmentioning

confidence: 99%

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

Yacoubi

Lyons

Cruz

et al. 2009

Nucleic Acids Research

153

198

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Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo.

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Crystal structure of the YciO protein from Escherichia coli

Cited by 21 publications

References 13 publications

Initial Proteome Analysis of Model MicroorganismHaemophilus influenzaeStrain Rd KW20

Initial Proteome Analysis of Model MicroorganismHaemophilus influenzaeStrain Rd KW20

Crystal structure of sulfolobus tokodaii sua5 complexed with L‐threonine and AMPPNP

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

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