4Y0W

YeaZ from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of YeaZ from Pseudomonas aeruginosa.

Vecchietti, D.Ferrara, S.Rusmini, R.Macchi, R.Milani, M.Bertoni, G.

(2016) Biochem Biophys Res Commun 470: 460-465

  • DOI: 10.1016/j.bbrc.2016.01.008
  • Primary Citation of Related Structures:  
    4Y0W

  • PubMed Abstract: 
  • The Pseudomonas aeruginosa PA3685 locus encodes a conserved protein that shares 49% sequence identity with Escherichia coli YeaZ, which was recently reported as involved in the biosynthesis of threonylcarbamoyl adenosine (t(6)A), a universal modified ...

    The Pseudomonas aeruginosa PA3685 locus encodes a conserved protein that shares 49% sequence identity with Escherichia coli YeaZ, which was recently reported as involved in the biosynthesis of threonylcarbamoyl adenosine (t(6)A), a universal modified tRNA nucleoside. Many YeaZ orthologues were reported as "essential for life" among various bacterial species, suggesting a critical role for both these proteins and for the t(6)A biosynthetic pathway. We provide here evidences that PA3685 protein (PaYeaZ) is essential. Additionally, we describe its purification, crystallization, and crystallographic structure. The crystal structure shows that PaYeaZ is composed of two domains one of which is the platform to form protein-protein interaction involved either in homodimeric assembly or in the formation of the multiprotein complex required for the synthesis of t(6)A. These features make the PaYeaZ protein a potential target candidate for the design of novel inhibitors able to hinder the complex formation and expected to abolish the crucial activity of t(6)A synthesis.


    Organizational Affiliation

    Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YeaZABCDE232Pseudomonas aeruginosa PAO579Mutation(s): 0 
Gene Names: A161_18155
Find proteins for A0A140UHA7 (Pseudomonas aeruginosa PAO579)
Explore A0A140UHA7 
Go to UniProtKB:  A0A140UHA7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.03α = 90
b = 198.443β = 90
c = 161.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-02-06 
  • Released Date: 2016-01-27 
  • Deposition Author(s): Milani, M.

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references