Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

Han, Gye Won; Yang, Xiang‐Lei; McMullan, Daniel; Chong, Yeeting E.; Krishna, S. Sri; Rife, Christopher L.; Weekes, Dana; Brittain, Scott M.; Abdubek, Polat; Ambing, Eileen; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Caruthers, J.M.; Chiu, Hsiu Ju; Clayton, Thomas; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C; Grzechnik, Slawomir K.; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Miller, Mitchell D.; Morse, Andrew; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; Bedem, H. van den; White, Aprilfawn; Wolf, Guenter; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc‐André; Schimmel, Paul; Wilson, Ian A.

doi:10.1107/s1744309110037619

Cited by 20 publications

(21 citation statements)

References 37 publications

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“…The mean age of patients of the included studies ranged from 1925 to 6027 years. Most articles included patients with all types of meniscal tears; however, two studies28 29 only included radial tears, two studies30 31 only horizontal tears, one study32 only included root-tears, one study33 only complex tears and one study34 only bucket-handle tears. Five studies excluded patients with a certain degree of chondral damage.…”

Section: Resultsmentioning

confidence: 99%

Can we predict the clinical outcome of arthroscopic partial meniscectomy? A systematic review

et al. 2017

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Section: Resultsmentioning

confidence: 99%

Can we predict the clinical outcome of arthroscopic partial meniscectomy? A systematic review

et al. 2017

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“…7). Only two currently known structures contain this type of binding site - PDB ID: 2G36 [67] and 3A04 (Tsuchiya, W., Fujimoto, Z., Hasegawa, T.; unpublished) - both tryptophan tRNA synthetases from thermophilic organisms. Given that most of the backbone amides that would normally contribute to electrostatic interactions with the cluster participate in intra-helical hydrogen bonds, other groups in the protein replace these missing interactions.…”

Section: Helical De Novo Designsmentioning

confidence: 99%

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Nanda

Senn

Pike

et al. 2016

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed.

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“…The TrpRS-A1 proteins appear to be restricted within CPR bacteria. The TrpRS-A2 proteins are predicted to chelate a [4Fe–4S] cluster through their four cysteine residues, like some bacterial and archaeal TrpRS proteins having a C-x22-C-x6-C-x2-C motif [38]. …”

Section: Resultsmentioning

confidence: 99%

Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

Mukai

Reynolds

Crnković

et al. 2017

Life

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The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyr and tRNATrp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code.

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Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

Abstract: The crystal structure of tryptophanyl-tRNA synthetase from T. maritima unexpectedly revealed an iron–sulfur cluster bound to the tRNA anticodon-binding region.

Cited by 20 publications

References 37 publications

Can we predict the clinical outcome of arthroscopic partial meniscectomy? A systematic review

Can we predict the clinical outcome of arthroscopic partial meniscectomy? A systematic review

Structural principles for computational and de novo design of 4Fe–4S metalloproteins

Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

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