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PDBsum entry 1yfr

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1yfr
Jmol
Contents
Protein chains
448 a.a. *
Ligands
ATP ×2
Metals
_MG ×6
Waters ×190
* Residue conservation analysis
PDB id:
1yfr
Name: Ligase
Title: Crystal structure of alanyl-tRNA synthetase in complex with atp and magnesium
Structure: Alanyl-tRNA synthetase. Chain: a, b. Synonym: alanine-tRNA ligase, alars. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: alas. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.194     R-free:   0.225
Authors: M.A.Swairjo,P.R.Schimmel
Key ref:
M.A.Swairjo and P.R.Schimmel (2005). Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc Natl Acad Sci U S A, 102, 988-993. PubMed id: 15657145 DOI: 10.1073/pnas.0409024102
Date:
03-Jan-05     Release date:   25-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67323  (SYA_AQUAE) -  Alanine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
867 a.a.
448 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.7  - Alanine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala)
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ L-alanine
+ tRNA(Ala)
= AMP
+ diphosphate
+ L-alanyl-tRNA(Ala)
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     alanyl-tRNA aminoacylation   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0409024102 Proc Natl Acad Sci U S A 102:988-993 (2005)
PubMed id: 15657145  
 
 
Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.
M.A.Swairjo, P.R.Schimmel.
 
  ABSTRACT  
 
The genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-tRNA synthetases. Amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. Although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. Paradoxically, although alanyl-tRNA synthetase activates glycine as well as alanine, the sterically larger (than alanine) serine is also misactivated. Here, we report crystal structures of an active fragment of Aquifex aeolicus alanyl-tRNA synthetase complexed, separately, with Mg2+-ATP, alanine, glycine, and serine. Ala and Gly are bound in similar orientations in a side-chain-accommodating pocket, where alpha-amino and carboxyl groups are stabilized by salt bridges, and the carboxyl by an H-bond from the side chain NH2 of Asn-194. In contrast, whereas the same two salt bridges stabilize bound Ser, H-bonding of the highly conserved (among class II tRNA synthetases) Asn-194 side chain NH2 to the Ser OH, instead of to the carboxyl, forces pocket expansion. Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser exclusion is broken because of selective pressure to retain Asn-194 for Mg2+-ATP and Ala binding.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. ATP binding by AlaRS. (A) Simulated annealed omit F[o] - F[c] electron density map (resolution, 2.15 Å; contour, 2.8 ) for the active site region of AlaRS[453]/Mg2+-ATP complex, superimposed on the refined model. The model for ATP, magnesium ions, and surrounding atoms within a sphere of 3.2 Å was omitted from map calculation. (B) Similar view showing active site residues involved in ATP or magnesium binding. Model colors are as in Fig. 1. Bound magnesium ions and water molecules are shown as gray and red spheres, respectively. For clarity, some water molecules and interactions with the ribose are not shown. (C) Schematic of the interactions between enzyme, ATP, and magnesium. Residues from motifs 2 and 3 are shown in orange and cyan, respectively. Residues in black belong to strands in the central -sheet of the active-site domain. Side chain conservation patterns among AlaRS sequences from 80 organisms are shown in brackets (percentage occurrence shown only for side chains present in >4% of the sequences). Side chains without adjacent bracketed numbers are invariant.
Figure 5.
Fig. 5. ATP-induced conformational changes in AlaRS[453] active site. Cyan ribbon and side chains, apo AlaRS[453]; yellow ribbon and colored side chains, complex with Mg2+-ATP.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179335 M.Guo, R.Shapiro, P.Schimmel, and X.L.Yang (2010).
Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase.
  Acta Crystallogr D Biol Crystallogr, 66, 243-250.  
20010690 M.Guo, Y.E.Chong, R.Shapiro, K.Beebe, X.L.Yang, and P.Schimmel (2009).
Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma.
  Nature, 462, 808-812.
PDB codes: 3hxu 3hxv 3hxw 3hxx 3hxy 3hxz 3hy0 3hy1
19423669 M.Naganuma, S.Sekine, R.Fukunaga, and S.Yokoyama (2009).
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
  Proc Natl Acad Sci U S A, 106, 8489-8494.
PDB codes: 2ztg 2zvf
19549823 M.Sokabe, T.Ose, A.Nakamura, K.Tokunaga, O.Nureki, M.Yao, and I.Tanaka (2009).
The structure of alanyl-tRNA synthetase with editing domain.
  Proc Natl Acad Sci U S A, 106, 11028-11033.
PDB codes: 2zze 2zzf 2zzg
19258309 R.A.Hellmann, and S.A.Martinis (2009).
Defects in transient tRNA translocation bypass tRNA synthetase quality control mechanisms.
  J Biol Chem, 284, 11478-11484.  
17303165 C.Liu, H.Gamper, S.Shtivelband, S.Hauenstein, J.J.Perona, and Y.M.Hou (2007).
Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase.
  J Mol Biol, 367, 1063-1078.  
17327676 R.Fukunaga, and S.Yokoyama (2007).
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 63, 390-400.
PDB code: 2e1b
  17329819 R.Fukunaga, and S.Yokoyama (2007).
Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 224-228.  
17027500 T.Crepin, A.Yaremchuk, M.Tukalo, and S.Cusack (2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
  Structure, 14, 1511-1525.
PDB codes: 2i4l 2i4m 2i4n 2i4o 2j3l 2j3m
16087889 M.Sokabe, A.Okada, M.Yao, T.Nakashima, and I.Tanaka (2005).
Molecular basis of alanine discrimination in editing site.
  Proc Natl Acad Sci U S A, 102, 11669-11674.
PDB codes: 1v7o 1wnu 1wxo
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.