1YIA

Crystal structure of tryptophanyl tRNA synthetase II from Deinococcus radiodurans in complex with 5-Hydroxy tryptophan.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Structure and activity of an aminoacyl-tRNA synthetase that charges tRNA with nitro-tryptophan.

Buddha, M.R., Crane, B.R.

(2005) Nat Struct Mol Biol 12: 274-275

  • DOI: https://doi.org/10.1038/nsmb907
  • Primary Citation of Related Structures:  
    1YI8, 1YIA

  • PubMed Abstract: 

    The most divergent of two tryptophanyl tRNA synthetases (TrpRS II) found in Deinococcus radiodurans interacts with a nitric oxide synthase protein that produces 4-nitro-tryptophan (4-NRP). TrpRS II efficiently charges transfer RNA(Trp) with 4-NRP and 5-hydroxy-tryptophan (5-HRP). The crystal structures of TrpRS II bound to tryptophan and 5-HRP reveal residue substitutions that accommodate modified indoles. A class of auxiliary bacterial TrpRSs conserve this capacity to charge tRNA with nonstandard amino acids.

    • Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tryptophanyl-tRNA synthetaseA [auth B],
B [auth A],
C		351Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: DR1093
EC: 6.1.1.2
UniProt
Find proteins for Q9RVD6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RVD6 
Go to UniProtKB:  Q9RVD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RVD6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HRP
Query on HRP
Download Ideal Coordinates CCD File 
D [auth B]5-HYDROXY-L-TRYPTOPHAN
C11 H12 N2 O3
LDCYZAJDBXYCGN-SECBINFHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.2α = 90
b = 58.4β = 96.5
c = 86.8γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Data collection
  • Version 1.4: 2018-02-07
    Changes: Experimental preparation
  • Version 1.5: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations