4Y0W | pdb_00004y0w

YeaZ from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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: https://doi.org/10.1016/j.bbrc.2016.01.008
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 125.25 kDa 
  • Atom Count: 8,084 
  • Modeled Residue Count: 1,053 
  • Deposited Residue Count: 1,160 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YeaZ
A, B, C, D, E
232Pseudomonas aeruginosa PAO579Mutation(s): 0 
Gene Names: A161_18155
UniProt
Find proteins for A0A140UHA7 (Pseudomonas aeruginosa PAO579)
Explore A0A140UHA7 
Go to UniProtKB:  A0A140UHA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140UHA7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
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

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations