PDBsum entry 1y42

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Ligase PDB id
Protein chain
370 a.a. *
Waters ×198
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Crystal structure of a c-terminally truncated cyt-18 protein
Structure: Tyrosyl-tRNA synthetase, mitochondrial. Chain: x. Fragment: nucleotide-binding fold, alpha helical domain. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes
Source: Neurospora crassa. Organism_taxid: 5141. Gene: cyt-18. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.95Å     R-factor:   0.179     R-free:   0.235
Authors: P.J.Paukstelis,R.Coon,L.Madabusi,J.Nowakowski,A.Monzingo,J.R A.M.Lambowitz
Key ref:
P.J.Paukstelis et al. (2005). A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface. Mol Cell, 17, 417-428. PubMed id: 15694342 DOI: 10.1016/j.molcel.2004.12.026
29-Nov-04     Release date:   15-Feb-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P12063  (SYYM_NEUCR) -  Tyrosine--tRNA ligase, mitochondrial
669 a.a.
370 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Tyrosine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
Bound ligand (Het Group name = TYR)
corresponds exactly
+ tRNA(Tyr)
+ diphosphate
+ L-tyrosyl-tRNA(Tyr)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     4 terms  


DOI no: 10.1016/j.molcel.2004.12.026 Mol Cell 17:417-428 (2005)
PubMed id: 15694342  
A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface.
P.J.Paukstelis, R.Coon, L.Madabusi, J.Nowakowski, A.Monzingo, J.Robertus, A.M.Lambowitz.
We determined a 1.95 A X-ray crystal structure of a C-terminally truncated Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) that functions in splicing group I introns. CYT-18's nucleotide binding fold and intermediate alpha-helical domains superimpose on those of bacterial TyrRSs, except for an N-terminal extension and two small insertions not found in nonsplicing bacterial enzymes. These additions surround the cyt-18-1 mutation site and are sites of suppressor mutations that restore splicing, but not synthetase activity. Highly constrained models based on directed hydroxyl radical cleavage assays show that the group I intron binds at a site formed in part by the three additions on the nucleotide binding fold surface opposite that which binds tRNATyr. Our results show how essential proteins can progressively evolve new functions.
  Selected figure(s)  
Figure 2.
Figure 2. Structure of CYT-18/ΔC424-669- and CYT-18-Specific Insertions(A) Stereo ribbon diagrams showing structural overlap of the nucleotide binding fold and α-helical domains of CYT-18/ΔC424-669 (purple) and B. stearothermophilus (yellow) TyrRS. The B. stearothermophilus TyrRS monomer structure (PDB ID: 3TS1) was superimposed on that of CYT-18 by least-squares fit of the Cα atoms of the nucleotide binding fold's central β sheet. CYT-18-specific insertions are in cyan.(B) Structure of the N-terminal extension. Amino acid residues that are highly conserved (>80%) in splicing-competent CYT-18 variants isolated from a library with partially randomized H0 sequences (Mohr et al., 2001) are shown with black side chains. The locations of the cyt-18-1 mutation, G127E, and second-site mutations that restore splicing, but not TyrRS activity are shown as black and yellow ribbon segments, respectively. Residues with green side chains are referred to in the text.(C) Structure of insertion II showing the location of N-terminal acidic and proline residues.
Figure 7.
Figure 7. Electrostatic Surface Potentials of CYT-18/ΔC424-669 and Bacterial TyrRSs(A) CYT-18/ΔC424-669 dimer structure shown in space-filling representation with calculated electrostatic surface potentials. The left shows the side of the protein with the TyrRS active site, and the right shows the opposite side. Positively charged regions are shown in blue, neutral regions are shown in white, and negatively charged regions are shown in red.(B and C) Same views of the B. stearothermophilus TyrRS (PDB ID: 4TS1) and T. thermophilus TyrRS (PDB ID: 1H3E).
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 17, 417-428) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21383132 G.D.Tocchini-Valentini, P.Fruscoloni, and G.P.Tocchini-Valentini (2011).
Evolution of introns in the archaeal world.
  Proc Natl Acad Sci U S A, 108, 4782-4787.  
19913030 A.B.Chadee, H.Bhaskaran, and R.Russell (2010).
Protein roles in group I intron RNA folding: the tyrosyl-tRNA synthetase CYT-18 stabilizes the native state relative to a long-lived misfolded structure without compromising folding kinetics.
  J Mol Biol, 395, 656-670.  
20126554 C.D.Duncan, and K.M.Weeks (2010).
The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs.
  PLoS One, 5, e8983.  
19910528 G.D.Tocchini-Valentini, P.Fruscoloni, and G.P.Tocchini-Valentini (2009).
Processing of multiple-intron-containing pretRNA.
  Proc Natl Acad Sci U S A, 106, 20246-20251.  
19393667 M.Del Campo, S.Mohr, Y.Jiang, H.Jia, E.Jankowsky, and A.M.Lambowitz (2009).
Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones.
  J Mol Biol, 389, 674-693.  
19622748 M.T.Boniecki, S.B.Rho, M.Tukalo, J.L.Hsu, E.P.Romero, and S.A.Martinis (2009).
Leucyl-tRNA synthetase-dependent and -independent activation of a group I intron.
  J Biol Chem, 284, 26243-26250.  
18388132 B.J.Kaspar, A.L.Bifano, and M.G.Caprara (2008).
A shared RNA-binding site in the Pet54 protein is required for translational activation and group I intron splicing in yeast mitochondria.
  Nucleic Acids Res, 36, 2958-2968.  
18522650 C.D.Hausmann, and M.Ibba (2008).
Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed.
  FEMS Microbiol Rev, 32, 705-721.  
18096186 G.Mohr, M.Del Campo, S.Mohr, Q.Yang, H.Jia, E.Jankowsky, and A.M.Lambowitz (2008).
Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro.
  J Mol Biol, 375, 1344-1364.  
18413600 P.J.Paukstelis, and A.M.Lambowitz (2008).
Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity.
  Proc Natl Acad Sci U S A, 105, 6010-6015.  
18172503 P.J.Paukstelis, J.H.Chen, E.Chase, A.M.Lambowitz, and B.L.Golden (2008).
Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA.
  Nature, 451, 94-97.
PDB code: 2rkj
18768647 Q.Vicens, P.J.Paukstelis, E.Westhof, A.M.Lambowitz, and T.R.Cech (2008).
Toward predicting self-splicing and protein-facilitated splicing of group I introns.
  RNA, 14, 2013-2029.  
17081564 C.Halls, S.Mohr, M.Del Campo, Q.Yang, E.Jankowsky, and A.M.Lambowitz (2007).
Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity.
  J Mol Biol, 365, 835-855.  
  17401211 L.Bonnefond, M.Frugier, E.Touzé, B.Lorber, C.Florentz, R.Giegé, J.Rudinger-Thirion, and C.Sauter (2007).
Tyrosyl-tRNA synthetase: the first crystallization of a human mitochondrial aminoacyl-tRNA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 338-341.  
16356725 Q.Vicens, and T.R.Cech (2006).
Atomic level architecture of group I introns revealed.
  Trends Biochem Sci, 31, 41-51.  
16116439 A.Longo, C.W.Leonard, G.S.Bassi, D.Berndt, J.M.Krahn, T.M.Hall, and K.M.Weeks (2005).
Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.
  Nat Struct Mol Biol, 12, 779-787.
PDB code: 2ab5
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.