5VXB

Crystal structure of Caulobacter crescentus ProXp-ala at 1.69 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Conformational and chemical selection by a trans-acting editing domain.

Danhart, E.M.Bakhtina, M.Cantara, W.A.Kuzmishin, A.B.Ma, X.Sanford, B.L.Kosutic, M.Goto, Y.Suga, H.Nakanishi, K.Micura, R.Foster, M.P.Musier-Forsyth, K.

(2017) Proc Natl Acad Sci U S A 114: E6774-E6783

  • DOI: 10.1073/pnas.1703925114
  • Primary Citation of Related Structures:  
    5VXB

  • PubMed Abstract: 
  • Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans -editing proteins ...

    Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans -editing proteins. ProXp-ala is a ubiquitous trans -editing enzyme that edits Ala-tRNA Pro , the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNA Pro and mischarged Ala-tRNA Ala is unclear. Deacylation assays using substrate analogs reveal that size discrimination is only one component of selectivity. We used NMR spectroscopy and sequence conservation to guide extensive site-directed mutagenesis of Caulobacter crescentus ProXp-ala, along with binding and deacylation assays to map specificity determinants. Chemical shift perturbations induced by an uncharged tRNA Pro acceptor stem mimic, microhelix Pro , or a nonhydrolyzable mischarged Ala-microhelix Pro substrate analog identified residues important for binding and deacylation. Backbone 15 N NMR relaxation experiments revealed dynamics for a helix flanking the substrate binding site in free ProXp-ala, likely reflecting sampling of open and closed conformations. Dynamics persist on binding to the uncharged microhelix, but are attenuated when the stably mischarged analog is bound. Computational docking and molecular dynamics simulations provide structural context for these findings and predict a role for the substrate primary α-amine group in substrate recognition. Overall, our results illuminate strategies used by a trans -editing domain to ensure acceptance of only mischarged Ala-tRNA Pro , including conformational selection by a dynamic helix, size-based exclusion, and optimal positioning of substrate chemical groups.


    Organizational Affiliation

    Center for RNA Biology, The Ohio State University, Columbus, OH 43210.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProXp-alaA, B, C171Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_0111
UniProt
Find proteins for Q9ABV9 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9ABV9 
Go to UniProtKB:  Q9ABV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ABV9
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.042α = 90
b = 67.733β = 118.62
c = 62.927γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM113656
Department of Energy (DOE, United States)United StatesGUP-51294

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence