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PDBsum entry 1o0b

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protein dna_rna ligands links
Ligase/RNA PDB id
1o0b
Jmol
Contents
Protein chain
529 a.a. *
DNA/RNA
Ligands
SO4 ×2
GLN
AMP
Waters ×144
* Residue conservation analysis
PDB id:
1o0b
Name: Ligase/RNA
Title: Crystal structure of l-glutamine and ampcpp bound to glutamine aminoacyl tRNA synthetase
Structure: Glutaminyl tRNA. Chain: b. Synonym: tRNA(gln). Transfer RNA-gln ii. Engineered: yes. Mutation: yes. Glutaminyl-tRNA synthetase. Chain: a. Synonym: glutamine--tRNA ligase. Glutamine tRNA synthetase. Glnrs.
Source: Synthetic: yes. Other_details: product of runoff t7 polymerase transcription from a double helical DNA template. Escherichia coli. Organism_taxid: 562. Gene: glns. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.216     R-free:   0.289
Authors: T.L.Bullock,J.J.Perona
Key ref:
T.L.Bullock et al. (2003). Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants. J Mol Biol, 328, 395-408. PubMed id: 12691748 DOI: 10.1016/S0022-2836(03)00305-X
Date:
20-Feb-03     Release date:   15-Apr-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.
529 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1016/S0022-2836(03)00305-X J Mol Biol 328:395-408 (2003)
PubMed id: 12691748  
 
 
Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants.
T.L.Bullock, N.Uter, T.A.Nissan, J.J.Perona.
 
  ABSTRACT  
 
The 2.5 A crystal structure of Escherichia coli glutaminyl-tRNA synthetase in a quaternary complex with tRNA(Gln), an ATP analog and glutamate reveals that the non-cognate amino acid adopts a distinct binding mode within the active site cleft. In contrast to the binding of cognate glutamine, one oxygen of the charged glutamate carboxylate group makes a direct ion-pair interaction with the strictly conserved Arg30 residue located in the first half of the dinucleotide fold domain. The nucleophilic alpha-carboxylate moiety of glutamate is mispositioned with respect to both the ATP alpha-phosphate and terminal tRNA ribose groups, suggesting that a component of amino acid discrimination resides at the catalytic step of the reaction. Further, the other side-chain carboxylate oxygen of glutamate is found in a position identical to that previously proposed to be occupied by the NH(2) group of the cognate glutamine substrate. At this position, the glutamate oxygen accepts hydrogen bonds from the hydroxyl moiety of Tyr211 and a water molecule. These findings demonstrate that amino acid specificity by GlnRS cannot arise from hydrogen bonds donated by the cognate glutamine amide to these same moieties, as previously suggested. Instead, Arg30 functions as a negative determinant to drive binding of non-cognate glutamate into a non-productive orientation. The poorly differentiated cognate amino acid-binding site in GlnRS may be a consequence of the late emergence of this enzyme from the eukaryotic lineage of glutamyl-tRNA synthetases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (A) Schematic drawing of a proposed network of hydrogen bonds in the amino acid-binding pocket of GlnRS when substrate glutamine is bound. Arrowheads point toward the hydrogen bond acceptor of each pair, and numerals indicate the distance in Å units between the two electronegative atoms of the pair, as estimated from this 2.3 Å crystal structure. The closest approach of Arg30 to the glutamine substrate is 4 Å. MC indicates main-chain. The donor-acceptor pairings and directions of the hydrogen bonds in this model are identical to those proposed by Rath et al.10 based on the structure of GlnRS bound to the QSI analog (except that WAT4 was not considered in that analysis). The correspondence between the nomenclature of the water molecules is: WAT1 corresponds to WAT1050 of Rath et al.10 WAT2 corresponds to WAT1052, WAT3 corresponds to WAT1136, and WAT4 corresponds to WAT1081. (B) Schematic drawing of a proposed network of hydrogen bonds in the amino acid-binding pocket of GlnRS when non-cognate glutamate is bound. Glu makes two additional hydrogen bonds with Arg30 and WAT1. Differences in proposed hydrogen-bonding structure to accommodate the acceptor oxygen atoms of Glu are (i) bifurcation of the Og hydrogen of Ser227. This hydrogen lies 2.3 Å from WAT1 and 2.6 Å from the Asp219 carboxylate and is thus well-positioned to bifurcate; in the structure bound to Glu, the hydrogen in the refined coordinates rotates toward WAT1, which is itself re-oriented to donate a proton to the substrate as depicted. (ii) One proton of WAT3 is now bifurcated between the Asp212 carboxylate and Asn236 main-chain acceptors (bottom). Rotation of this water by graphics modeling shows that one proton can be oriented midway between the two acceptors at 2.6 Å distance from each, while the second proton then points in-line toward WAT2. This orients the two acceptor positions generally toward WAT4.
Figure 4.
Figure 4. Time-course for glutamylation of E. coli tRNA[2]^Gln by GlnRS. The inset shows a thin-layer chromatography plate in which misacylated Glu-AMP is formed to approximately 50% aminoacylation levels (see Materials and Methods for details). The % aminoacylation on the ordinate is derived from the ratio of intensities of the spots corresponding to Glu-AMP and AMP (right).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 395-408) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22683997 A.Palencia, T.Crépin, M.T.Vu, T.L.Lincecum, S.A.Martinis, and S.Cusack (2012).
Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase.
  Nat Struct Mol Biol, 19, 677-684.
PDB codes: 4aq7 4arc 4ari 4as1
21397189 A.Rodríguez-Hernández, and J.J.Perona (2011).
Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.
  Structure, 19, 386-396.  
20139416 M.G.Gagnon, Y.I.Boutorine, and S.V.Steinberg (2010).
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
  Nucleic Acids Res, 38, 3441-3453.  
20601684 O.Nureki, P.O'Donoghue, N.Watanabe, A.Ohmori, H.Oshikane, Y.Araiso, K.Sheppard, D.Söll, and R.Ishitani (2010).
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation.
  Nucleic Acids Res, 38, 7286-7297.
PDB code: 3aii
19128026 E.M.Corigliano, and J.J.Perona (2009).
Architectural underpinnings of the genetic code for glutamine.
  Biochemistry, 48, 676-687.  
19179361 W.Tsuchiya, and T.Hasegawa (2009).
Molecular recognition of tryptophan tRNA by tryptophanyl-tRNA synthetase from Aeropyrum pernix K1.
  J Biochem, 145, 635-641.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
18241795 K.Sheppard, P.M.Akochy, and D.Söll (2008).
Assays for transfer RNA-dependent amino acid biosynthesis.
  Methods, 44, 139-145.  
18267971 R.L.Sherrer, J.M.Ho, and D.Söll (2008).
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase.
  Nucleic Acids Res, 36, 1871-1880.  
18174226 R.L.Sherrer, P.O'Donoghue, and D.Söll (2008).
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.
  Nucleic Acids Res, 36, 1247-1259.  
18559341 S.I.Hauenstein, and J.J.Perona (2008).
Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei.
  J Biol Chem, 283, 22007-22017.  
18559342 S.I.Hauenstein, Y.M.Hou, and J.J.Perona (2008).
The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity.
  J Biol Chem, 283, 21997-22006.  
18241789 S.Ledoux, and O.C.Uhlenbeck (2008).
[3'-32P]-labeling tRNA with nucleotidyltransferase for assaying aminoacylation and peptide bond formation.
  Methods, 44, 74-80.  
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
18158303 Y.Araiso, S.Palioura, R.Ishitani, R.L.Sherrer, P.O'Donoghue, J.Yuan, H.Oshikane, N.Domae, J.Defranco, D.Söll, and O.Nureki (2008).
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation.
  Nucleic Acids Res, 36, 1187-1199.
PDB code: 2z67
17360621 A.Ambrogelly, S.Gundllapalli, S.Herring, C.Polycarpo, C.Frauer, and D.Söll (2007).
Pyrrolysine is not hardwired for cotranslational insertion at UAG codons.
  Proc Natl Acad Sci U S A, 104, 3141-3146.  
17447878 I.A.Vasil'eva, and N.A.Moor (2007).
Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition.
  Biochemistry (Mosc), 72, 247-263.  
17329242 K.Sheppard, P.M.Akochy, J.C.Salazar, and D.Söll (2007).
The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGln.
  J Biol Chem, 282, 11866-11873.  
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
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.  
17267409 S.Herring, A.Ambrogelly, C.R.Polycarpo, and D.Söll (2007).
Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase.
  Nucleic Acids Res, 35, 1270-1278.  
17158446 T.F.Chou, and C.R.Wagner (2007).
Lysyl-tRNA synthetase-generated lysyl-adenylate is a substrate for histidine triad nucleotide binding proteins.
  J Biol Chem, 282, 4719-4727.  
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.  
16864571 S.Hati, B.Ziervogel, J.Sternjohn, F.C.Wong, M.C.Nagan, A.E.Rosen, P.G.Siliciano, J.W.Chihade, and K.Musier-Forsyth (2006).
Pre-transfer editing by class II prolyl-tRNA synthetase: role of aminoacylation active site in "selective release" of noncognate amino acids.
  J Biol Chem, 281, 27862-27872.  
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.  
15614972 M.A.Deniziak, C.Sauter, H.D.Becker, R.Giegé, and D.Kern (2004).
Crystallization and preliminary X-ray characterization of the atypical glutaminyl-tRNA synthetase from Deinococcus radiodurans.
  Acta Crystallogr D Biol Crystallogr, 60, 2361-2363.  
15452355 N.T.Uter, and J.J.Perona (2004).
Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics.
  Proc Natl Acad Sci U S A, 101, 14396-14401.  
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
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.