spacer
spacer

PDBsum entry 1nyl

Go to PDB code: 
protein links
Ligase PDB id
1nyl
Jmol
Contents
Protein chain
523 a.a. *
Waters ×72
* Residue conservation analysis
PDB id:
1nyl
Name: Ligase
Title: Unliganded glutaminyl-tRNA synthetase
Structure: Glutaminyl-tRNA synthetase. Chain: a. Synonym: glutamine--tRNA ligase, glnrs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: glns. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.251     R-free:   0.327
Authors: L.D.Sherlin,J.P.Perona
Key ref:
L.D.Sherlin and J.J.Perona (2003). tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase. Structure, 11, 591-603. PubMed id: 12737824 DOI: 10.1016/S0969-2126(03)00074-1
Date:
12-Feb-03     Release date:   25-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00962  (SYQ_ECOLI) -  Glutamine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
554 a.a.
523 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.18  - Glutamine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl- tRNA(Gln)
ATP
+ L-glutamine
+ tRNA(Gln)
= AMP
+ diphosphate
+ L-glutaminyl- tRNA(Gln)
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     translation   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(03)00074-1 Structure 11:591-603 (2003)
PubMed id: 12737824  
 
 
tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase.
L.D.Sherlin, J.J.Perona.
 
  ABSTRACT  
 
The crystal structure of ligand-free E. coli glutaminyl-tRNA synthetase (GlnRS) at 2.4 A resolution shows that substrate binding is essential to construction of a catalytically proficient active site. tRNA binding generates structural changes throughout the enzyme, repositioning key active site peptides that bind glutamine and ATP. The structure gives insight into longstanding questions regarding the tRNA dependence of glutaminyl adenylate formation, the coupling of amino acid and tRNA selectivities, and the roles of specific pathways for transmission of tRNA binding signals to the active site. Comparative analysis of the unliganded and tRNA-bound structures shows, in detail, how flexibility is built into the enzyme architecture and suggests that the induced-fit transitions are a key underlying determinant of both amino acid and tRNA specificity.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Substrate Juxtaposition by Induced Fit(A) Stereo view of enzyme conformational changes in the vicinity of the tRNA 3'-end. The tRNA-bound and unliganded enzymes are superimposed on the basis of equivalent residues in the DNF domains (see text). tRNA, dark blue; unliganded enzyme, light blue; complexed enzyme, gray (DNF domain) and pink (ABD). Dotted red lines indicate hydrogen bonds observed in the GlnRS-tRNA complex. QSI inhibitor from the complexed structure, red.(B) Stereo view of enzyme conformational changes in the active site, with structures superimposed as in (A). Complexed enzyme, gray; unliganded enzyme, blue; QSI inhibitor, red. The disorder in the surface loop at Val71 in the unliganded enzyme is shown by the dotted blue line (right). Dotted red lines indicate hydrogen bonds observed in the GlnRS-tRNA complex.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 591-603) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397189 A.Rodríguez-Hernández, and J.J.Perona (2011).
Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.
  Structure, 19, 386-396.  
19128026 E.M.Corigliano, and J.J.Perona (2009).
Architectural underpinnings of the genetic code for glutamine.
  Biochemistry, 48, 676-687.  
19187230 G.L.Igloi, and E.Schiefermayr (2009).
Amino acid discrimination by arginyl-tRNA synthetases as revealed by an examination of natural specificity variants.
  FEBS J, 276, 1307-1318.  
18755841 C.M.Zhang, C.Liu, T.Christian, H.Gamper, J.Rozenski, D.Pan, J.B.Randolph, E.Wickstrom, B.S.Cooperman, and Y.M.Hou (2008).
Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end.
  RNA, 14, 2245-2253.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
18477696 T.L.Bullock, A.Rodríguez-Hernández, E.M.Corigliano, and J.J.Perona (2008).
A rationally engineered misacylating aminoacyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 7428-7433.
PDB codes: 2rd2 2re8
17284460 M.Deniziak, C.Sauter, H.D.Becker, C.A.Paulus, R.Giegé, and D.Kern (2007).
Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.
  Nucleic Acids Res, 35, 1421-1431.
PDB code: 2hz7
17510965 M.E.Budiman, M.H.Knaggs, J.S.Fetrow, and R.W.Alexander (2007).
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.
  Proteins, 68, 670-689.  
17937916 M.Kapustina, V.Weinreb, L.Li, B.Kuhlman, and C.W.Carter (2007).
A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase.
  Structure, 15, 1272-1284.  
17444518 R.Sathyapriya, and S.Vishveshwara (2007).
Structure networks of E. coli glutaminyl-tRNA synthetase: effects of ligand binding.
  Proteins, 68, 541-550.  
17378584 S.W.Lue, and S.O.Kelley (2007).
A single residue in leucyl-tRNA synthetase affecting amino acid specificity and tRNA aminoacylation.
  Biochemistry, 46, 4466-4472.  
16734422 N.T.Uter, and J.J.Perona (2006).
Active-site assembly in glutaminyl-tRNA synthetase by tRNA-mediated induced fit.
  Biochemistry, 45, 6858-6865.  
15845536 I.Gruic-Sovulj, N.Uter, T.Bullock, and J.J.Perona (2005).
tRNA-dependent aminoacyl-adenylate hydrolysis by a nonediting class I aminoacyl-tRNA synthetase.
  J Biol Chem, 280, 23978-23986.
PDB code: 1zjw
15845537 N.T.Uter, I.Gruic-Sovulj, and J.J.Perona (2005).
Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase.
  J Biol Chem, 280, 23966-23977.  
16251366 R.Powers, N.Mirkovic, S.Goldsmith-Fischman, T.B.Acton, Y.Chiang, Y.J.Huang, L.Ma, P.K.Rajan, J.R.Cort, M.A.Kennedy, J.Liu, B.Rost, B.Honig, D.Murray, and G.T.Montelione (2005).
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes.
  Protein Sci, 14, 2849-2861.
PDB code: 1rzw
14747465 J.Levengood, S.F.Ataide, H.Roy, and M.Ibba (2004).
Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases.
  J Biol Chem, 279, 17707-17714.  
15489861 S.Hauenstein, C.M.Zhang, Y.M.Hou, and J.J.Perona (2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 1134-1141.
PDB code: 1u0b
15100435 W.H.McClain, K.Gabriel, D.Lee, and S.Otten (2004).
Structure-function analysis of tRNA(Gln) in an Escherichia coli knockout strain.
  RNA, 10, 795-804.  
12737813 J.Cavarelli (2003).
Pushing induced fit to its limits: tRNA-dependent active site assembly in class I aminoacyl-tRNA synthetases.
  Structure, 11, 484-486.  
14530451 R.Banerjee, A.K.Mandal, R.Saha, S.Guha, S.Samaddar, A.Bhattacharyya, and S.Roy (2003).
Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases.
  Nucleic Acids Res, 31, 6035-6042.  
14690419 R.Geslain, G.Bey, J.Cavarelli, and G.Eriani (2003).
Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
  Biochemistry, 42, 15092-15101.  
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 codes are shown on the right.