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Title: Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gky1211· OSTI ID:1499769
 [1];  [2];  [3];  [1];  [1];  [3];  [4]; ORCiD logo [5]
  1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
  2. Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
  3. Institute of Organic Chemistry at Leopold Franzens University, A-6020 Innsbruck, Austria
  4. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA
  5. Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA

Research Organization:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
NIHFOREIGN
OSTI ID:
1499769
Journal Information:
Nucleic Acids Research, Vol. 47, Issue 4; ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
ENGLISH

References (69)

Gonadotropin-releasing-hormone-receptor antagonists journal November 2001
Translation Elongation by a Hybrid Ribosome in Which Proteins at the GTPase Center of the Escherichia coli Ribosome Are Replaced with Rat Counterparts journal November 2001
Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome journal February 2010
Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements journal September 2006
The Catalytic Properties of Tyrosyl Ribonucleic Acid Synthetases from Escherichia coli and Bacillus subtilis journal May 1966
Atomic Mutagenesis of the Ribosome: Towards a Molecular Understanding of Translation journal May 2013
Analysis of Predictions for the Catalytic Mechanism of Ribosomal Peptidyl Transfer journal June 2006
Ribosomal crystallography: a flexible nucleotide anchoring tRNA translocation, facilitates peptide-bond formation, chirality discrimination and antibiotics synergism journal April 2004
Efficient Access to Nonhydrolyzable Initiator tRNA Based on the Synthesis of 3′-Azido-3′-Deoxyadenosine RNA journal August 2010
Separation and sensitive detection of D-amino acids in biological matrices journal June 2009
Incorporation of β-amino acids into dihydrofolate reductase by ribosomes having modifications in the peptidyltransferase center journal March 2013
Expanding and reprogramming the genetic code journal October 2017
Recent Updates on DTD (D-Tyr-tRNATyr Deacylase): An Enzyme Essential for Fidelity and Quality of Protein Synthesis journal April 2016
Antimicrobial Activity and Stability to Proteolysis of Small Linear Cationic Peptides with D-Amino Acid Substitutions journal November 2002
Bacterial synthesis of d-amino acids journal April 2014
Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria journal August 2007
Altering the Enantioselectivity of Tyrosyl-tRNA Synthetase by Insertion of a Stereospecific Editing Domain journal March 2016
Engineered Ribosomes for Basic Science and Synthetic Biology journal June 2018
Native Chemical Ligation of Hydrolysis-Resistant 3′-Peptidyl–tRNA Mimics journal November 2011
Protein synthesis by ribosomes with tethered subunits journal July 2015
Structural Insights into the Roles of Water and the 2′ Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction journal November 2005
Discrimination between D- and L-tyrosyl transfer ribonucleic acids in peptide chain elongation journal December 1981
XDS journal January 2010
Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids journal June 2015
Upgrading protein synthesis for synthetic biology journal September 2013
Gc-ms analysis of diaminopimelic acid stereoisomers and amino acid enantiomers in rumen bacteria journal February 1999
The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center journal April 2015
A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest journal July 2016
Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids journal November 2016
An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA journal November 2005
Biogenesis of d -amino acid containing peptides/proteins: where, when and how? journal June 2014
Desmopressin in the treatment of nocturia: clinical evidence and experience journal August 2013
Ribosome Subunit Stapling for Orthogonal Translation in E.coli journal August 2015
EP 60761- and EP 50885-induced penile erection: structure–activity studies and comparison with apomorphine, oxytocin and N-methyl-D-aspartic acid journal October 2000
Natural Occurrence and Industrial Applications of d-Amino Acids: An Overview journal June 2010
PRODRG : a tool for high-throughput crystallography of protein–ligand complexes journal July 2004
Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the ω and rib-1 loci journal May 1980
D-Tryptophan-6 analog of luteinizing hormone-releasing hormone as a protective agent against testicular damage caused by cyclophosphamide in baboons. journal May 1985
How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis journal May 2012
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome journal April 2009
Crystal Structures of the uL3 Mutant Ribosome: Illustration of the Importance of Ribosomal Proteins for Translation Efficiency journal May 2016
Outwitting EF-Tu and the ribosome: translation with d-amino acids journal May 2015
Coot model-building tools for molecular graphics journal November 2004
An all D-amino acid opioid peptide with central analgesic activity from a combinatorial library journal December 1994
Consecutive Elongation of D-Amino Acids in Translation journal January 2017
Molecular insights into protein synthesis with proline residues journal October 2016
An orthogonal ribosome-tRNA pair via engineering of the peptidyl transferase center journal June 2014
Metabolism of d-Aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae Cells journal July 2000
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Emerging knowledge of regulatory roles of d-amino acids in bacteria journal December 2010
In Vivo Biosynthesis of a β-Amino Acid-Containing Protein journal January 2016
Logical engineering of D-arm and T-stem of tRNA that enhances d-amino acid incorporation journal November 2017
Construction of Modified Ribosomes for Incorporation of d -Amino Acids into Proteins journal December 2006
The Puromycin Route to Assess Stereo- and Regiochemical Constraints on Peptide Bond Formation in Eukaryotic Ribosomes journal July 2003
Altered ribosomal RNA genes in mitochondria from mammalian cells with chloramphenicol resistance journal April 1981
A network of orthogonal ribosome·mRNA pairs journal July 2005
Formation of d-Tyrosyl-tRNA Tyr Accounts for the Toxicity of d-Tyrosine toward Escherichia coli journal August 2004
Adding New Chemistries to the Genetic Code journal June 2010
Non-Hydrolyzable RNA-Peptide Conjugates: A Powerful Advance in the Synthesis of Mimics for 3′-Peptidyl tRNA Termini journal May 2009
Reevaluation of the d -Amino Acid Compatibility with the Elongation Event in Translation journal January 2013
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome journal August 2014
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly journal March 2015
Enhanced d -Amino Acid Incorporation into Protein by Modified Ribosomes journal June 2003
Structure of the Yeast Mitochondrial Large Ribosomal Subunit journal March 2014
Structure of the 70S Ribosome Complexed with mRNA and tRNA journal September 2006
Structural insights into peptide bond formation journal August 2002
Phaser crystallographic software journal July 2007
Initiating translation with D-amino acids journal May 2008
Hyperactive Editing Domain Variants Switch the Stereospecificity of Tyrosyl-tRNA Synthetase journal April 2016