The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N6-Threonylcarbamoyladenosine Dehydratase Activity

Journal of Molecular Biology

Volumn 427, Issue 19, 2015, Pages 3074-3085

  Kim, Sunmin ^a   Lee, Hyuk ^b   Park, Sangyoun ^a  

^a Soongsil University   (South Korea)

^b Korea Research Institute of Chemical Technology   (South Korea)

Author keywords

CsdL; N6 threonylcarbamoyladenosine dehydratase; RNA modification; structural biology; TcdA

Indexed keywords

ADENOSINE TRIPHOSPHATE; DIMER; ESCHERICHIA COLI PROTEIN; ESCHERICHIA COLI TCDA PROTEIN; HOMODIMER; HYDROLYASE; MEMBRANE PROTEIN; MOLYBDOPTERIN; N 6 THREONYLCARBAMOYLADENOSINE DEHYDRATASE; THIAMINE; TRANSFER RNA; UNCLASSIFIED DRUG; ADENOSINE; CSDL PROTEIN, E COLI; N(6)-(N-THREONYLCARBONYL)ADENOSINE; UBIQUITIN PROTEIN LIGASE;

ADENYLATION; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; RNA BINDING; SEQUENCE ALIGNMENT; SURFACE PROPERTY; ANALOGS AND DERIVATIVES; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; X RAY CRYSTALLOGRAPHY;

ADENOSINE; ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HYDRO-LYASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; RNA, TRANSFER; SEQUENCE ALIGNMENT; UBIQUITIN-ACTIVATING ENZYMES;

EID: 84941934047     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2015.06.005     Document Type: Article

References (20)

1. E.G. Mueller Trafficking in persulfides: delivering sulfur in biosynthetic pathways Nat Chem Biol 2 2006 185 194
2. H. Mihara, T. Kurihara, T. Yoshimura, K. Soda, and N. Esaki Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Gene cloning, purification, and characterization of a novel pyridoxal enzyme J Biol Chem 272 1997 22417 22424
3. V. Trotter, D. Vinella, L. Loiseau, S. Ollagnier de Choudens, M. Fontecave, and F. Barras The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein Mol Microbiol 74 2009 1527 1542
4. H.M. Bolstad, D.J. Botelho, and M.J. Wood Proteomic analysis of protein-protein interactions within the cysteine sulfinate desulfinase Fe-S cluster biogenesis system J Proteome Res 9 2010 5358 5369
5. S. Kim, and S.Y. Park Structural changes during cysteine desulfurase CsdA and sulfur-acceptor CsdE interactions provide insight into the trans-persulfuration J Biol Chem 288 2013 27172 27180
6. M.P. Schweizer, G.B. Chheda, L. Baczynskyj, and R.H. Hall Aminoacyl nucleosides. VII. N-(Purin-6-ylcarbamoyl)threonine. A new component of transfer ribonucleic acid Biochemistry 8 1969 3283 3289
7. F.V. Murphy, V. Ramakrishnan, A. Malkiewicz, and P.F. Agris The role of modifications in codon discrimination by tRNALys UUU Nat Struct Mol Biol 11 2004 1186 1191
8. B. El Yacoubi, M. Bailly, and V. de Crecy-Lagard Biosynthesis and function of posttranscriptional modifications of transfer RNAs Annu Rev Genet 46 2012 69 95
9. 6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification Nat Chem Biol 9 2013 105 111
10. M.W. Lake, M.M. Wuebbens, K.V. Rajagopalan, and H. Schindelin Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex Nature 414 2001 325 329
11. C. Lehmann, T.P. Begley, and S.E. Ealick Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis Biochemistry 45 2006 11 19
12. D.M. Duda, H. Walden, J. Sfondouris, and B.A. Schulman Structural analysis of Escherichia coli ThiF J Mol Biol 349 2005 774 786
13. L. Holm, and P. Rosenström Dali server: conservation mapping in 3D Nucleic Acids Res 38 2010 W545 W549
14. 6-threonylcarbamoyladenosine dehydratase Acta Crystallogr F Struct Biol Commun 70 2014 1517 1520
15. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol 276 1997 307 326
16. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, N. Echols, and et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr D Biol Crystallogr 66 2010 213 221
17. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr D Biol Crystallogr 60 2004 2126 2132
18. A.A. Vagin, R.A. Steiner, A.A. Lebedev, L. Potterton, S. McNicholas, F. Long, and et al. REFMAC5 dictionary: organisation of prior chemical knowledge and guidelines for its use Acta Crystallogr D Biol Crystallogr 60 2004 2284 2295
19. J. Berman, S. Eisenberg, and B.K. Tye An agarose gel electrophoresis assay for the detection of DNA-binding activities in yeast cell extracts Methods Enzymol 155 1987 528 537
20. M. López-Estepa, A. Ardá, M. Savko, A. Round, W.E. Shepard, M. Bruix, and et al. The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily PLoS One 10 2015 e0118606