2RHQ

PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Rational protein engineering in action: the first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus.

Evdokimov, A.G., Mekel, M., Hutchings, K., Narasimhan, L., Holler, T., McGrath, T., Beattie, B., Fauman, E., Yan, C., Heaslet, H., Walter, R., Finzel, B., Ohren, J., McConnell, P., Braden, T., Sun, F., Spessard, C., Banotai, C., Al-Kassim, L., Ma, W., Wengender, P., Kole, D., Garceau, N., Toogood, P., Liu, J.

(2008) J Struct Biol 162: 152-169

  • DOI: https://doi.org/10.1016/j.jsb.2007.11.002
  • Primary Citation of Related Structures:  
    2RHQ, 2RHS

  • PubMed Abstract: 

    • In this article, we describe for the first time the high-resolution crystal structure of a phenylalanine tRNA synthetase from the pathogenic bacterium Staphylococcus haemolyticus. We demonstrate the subtle yet important structural differences between this enzyme and the previously described Thermus thermophilus ortholog ...

    In this article, we describe for the first time the high-resolution crystal structure of a phenylalanine tRNA synthetase from the pathogenic bacterium Staphylococcus haemolyticus. We demonstrate the subtle yet important structural differences between this enzyme and the previously described Thermus thermophilus ortholog. We also explain the structure-activity relationship of several recently reported inhibitors. The native enzyme crystals were of poor quality--they only diffracted X-rays to 3-5A resolution. Therefore, we have executed a rational surface mutagenesis strategy that has yielded crystals of this 2300-amino acid multidomain protein, diffracting to 2A or better. This methodology is discussed and contrasted with the more traditional domain truncation approach.

    Organizational Affiliation: 

    Pfizer Global Research & Development, Michigan Laboratories, Ann Arbor, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. artem@xtals.org



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase alpha chain294Staphylococcus haemolyticusMutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
UniProt
Find proteins for Q4L5E3 (Staphylococcus haemolyticus (strain JCSC1435))
Explore Q4L5E3 
Go to UniProtKB:  Q4L5E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4L5E3
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase beta chain795Staphylococcus haemolyticusMutation(s): 6 
Gene Names: pheT
EC: 6.1.1.20
UniProt
Find proteins for Q4L5E4 (Staphylococcus haemolyticus (strain JCSC1435))
Explore Q4L5E4 
Go to UniProtKB:  Q4L5E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4L5E4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAX
Query on GAX
Download Ideal Coordinates CCD File 
D [auth A]1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea
C19 H20 N6 O3 S2
NJPVZSIGDRLLTD-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 249.312α = 90
b = 87.602β = 100.44
c = 61.072γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

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: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations