2RE8

Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMYL)-SULFAMOYL]ADENOSINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A rationally engineered misacylating aminoacyl-tRNA synthetase.

Bullock, T.L., Rodriguez-Hernandez, A., Corigliano, E.M., Perona, J.J.

(2008) Proc Natl Acad Sci U S A 105: 7428-7433

  • DOI: 10.1073/pnas.0711812105
  • Primary Citation of Related Structures:  
    2RD2, 2RE8

  • PubMed Abstract: 

    • Information transfer from nucleic acid to protein is mediated by aminoacyl-tRNA synthetases, which catalyze the specific pairings of amino acids with transfer RNAs. Despite copious sequence and structural information on the 22 tRNA synthetase families, little is known of the enzyme signatures that specify amino acid selectivities ...

    Information transfer from nucleic acid to protein is mediated by aminoacyl-tRNA synthetases, which catalyze the specific pairings of amino acids with transfer RNAs. Despite copious sequence and structural information on the 22 tRNA synthetase families, little is known of the enzyme signatures that specify amino acid selectivities. Here, we show that transplanting a conserved arginine residue from glutamyl-tRNA synthetase (GluRS) to glutaminyl-tRNA synthetase (GlnRS) improves the K(M) of GlnRS for noncognate glutamate. Two crystal structures of this C229R GlnRS mutant reveal that a conserved twin-arginine GluRS amino acid identity signature cannot be incorporated into GlnRS without disrupting surrounding protein structural elements that interact with the tRNA. Consistent with these findings, we show that cumulative replacement of other primary binding site residues in GlnRS, with those of GluRS, only slightly improves the ability of the GlnRS active site to accommodate glutamate. However, introduction of 22 amino acid replacements and one deletion, including substitution of the entire primary binding site and two surface loops adjacent to the region disrupted in C229R, improves the capacity of Escherichia coli GlnRS to synthesize misacylated Glu-tRNA(Gln) by 16,000-fold. This hybrid enzyme recapitulates the function of misacylating GluRS enzymes found in organisms that synthesize Gln-tRNA(Gln) by an alternative pathway. These findings implicate the RNA component of the contemporary GlnRS-tRNA(Gln) complex in mediating amino acid specificity. This role for tRNA may persist as a relic of primordial cells in which the evolution of the genetic code was driven by RNA-catalyzed amino acid-RNA pairing.

    Related Citations: 
    • Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.
      Sherlin, L.D., Bullock, T.L., Nissan, T.A., Perona, J.J., Lariviere, F.J., Uhlenbeck, O.C., Scaringe, S.A.
      (2001) RNA 7: 1671
    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106-9510, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutaminyl-tRNA synthetaseB [auth A]556Escherichia coliMutation(s): 1 
Gene Names: glnS
EC: 6.1.1.18
UniProt
Find proteins for P00962 (Escherichia coli (strain K12))
Explore P00962 
Go to UniProtKB:  P00962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00962
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Glutamine tRNAA [auth B]75N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSU
Query on GSU
Download Ideal Coordinates CCD File 
E [auth A]O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
C15 H21 N7 O9 S
YBRKRYFZKHICLS-WERHYGNASA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.142α = 90
b = 92.907β = 90
c = 115.512γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations