1JJC

Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.

Fishman, R.Ankilova, V.Moor, N.Safro, M.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1534-1544

  • DOI: 10.1107/s090744490101321x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus, a class II aminoacyl-tRNA synthetase, complexed with phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 A resolution. Crystals of native PheRS were soaked in ...

    The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus, a class II aminoacyl-tRNA synthetase, complexed with phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 A resolution. Crystals of native PheRS were soaked in a solution containing phenylalanine and ATP in the presence of Mn(2+) ions. The first step of the aminoacylation reaction proceeds within the crystals, resulting in Phe-AMP formation at the active site. Specific recognition of the phenylalanine portion of the Phe-AMP is achieved by interactions of the phenyl ring of Phe-AMP with two neighbouring residues, Phealpha258 and Phealpha260. No manganese ions were observed within the active site; their role in the formation of the transition state may be assigned to a number of polar residues and water molecules. In the anomalous Fourier difference map, a divalent metal ion was detected at the interface of the alpha- and beta-subunits at a short distance from motif 3 residues participating in the substrate binding. A sulfate ion, which was identified on the protein surface, may mediate the interactions of PheRS with DNA. Visible conformational changes were detected in the active-site area adjacent to the position of the Phe-AMP, compared with the structure of PheRS complexed with a synthetic adenylate analogue (phenylalaninyl-adenylate). Based on the known structures of the substrate-free enzyme and its complexes with various ligands, a general scheme for the phenylalanylation mechanism is proposed.


    Related Citations: 
    • Structure pf phenylalanyl-tRNA synthetase from Thermus thermophilus
      Mosyak, L., Reshetnikova, L., Goldgur, Y., Delarue, M., Safro, M.
      (1995) Nat Struct Biol 2: 537
    • The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus complexed with cognate tRNA-Phe
      Goldgur, Y., Mosyak, L., Reshetnikova, L., Ankilova, V., Khodyreva, S., Safro, M.
      (1997) Structure 5: 59
    • Crystal Structures of phenylalnyl-tRNA synthetase complexed with phenylalanine and phenylalanyl-adenylate analogue
      Reshenikova, L., Moor, N., Lavrik, O., Vassyliev, D.
      (1999) J Mol Biol 287: 555

    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAINA350Thermus thermophilus HB8Mutation(s): 0 
Gene Names: pheSTTHA1958
EC: 6.1.1.20
Find proteins for Q5SGX2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SGX2 
Go to UniProtKB:  Q5SGX2
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHENYLALANYL-TRNA SYNTHETASE BETA CHAINB785Thermus thermophilus HB8Mutation(s): 0 
Gene Names: pheTTTHA1959
EC: 6.1.1.20
Find proteins for Q5SGX1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SGX1 
Go to UniProtKB:  Q5SGX1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FA5
Query on FA5

Download CCD File 
A
ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE]
C19 H23 N6 O8 P
ZFNOOEXYTZPIQS-URQYDQELSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.4α = 90
b = 173.4β = 90
c = 138.4γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance