3ZEU

Structure of a Salmonella typhimurium YgjD-YeaZ heterodimer bound to ATPgammaS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.653 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Dimer of Two Essential Salmonella Typhimurium Proteins, Ygjd & Yeaz and Calorimetric Evidence for the Formation of a Ternary Ygjd-Yeaz-Yjee Complex.

Nichols, C.E.Lamb, H.K.Thompson, P.Omari, K.E.Lockyer, M.Charles, I.Hawkins, A.R.Stammers, D.K.

(2013) Protein Sci. 22: 628

  • DOI: 10.1002/pro.2247
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • YgjD from COG0533 is amongst a small group of highly conserved proteins present in all three domains of life. Various roles and biochemical functions (including sialoprotease and endonuclease activities) have been ascribed to YgjD and orthologs, the ...

    YgjD from COG0533 is amongst a small group of highly conserved proteins present in all three domains of life. Various roles and biochemical functions (including sialoprotease and endonuclease activities) have been ascribed to YgjD and orthologs, the most recent, however, is involvement in the post transcriptional modification of certain tRNAs by formation of N6-threonyl-adenosine (t⁶A) at position 37. In bacteria, YgjD is essential and along with YeaZ, YjeE, and YrdC has been shown to be 'necessary and sufficient' for the tRNA modification. To further define interactions and possible roles for some of this set of proteins we have undertaken structural and biochemical studies. We show that formation of the previously reported heterodimer of YgjD-YeaZ involves ordering of the C-terminal region of YeaZ which extends along the surface of YgjD in the crystal structure. ATPγS or AMP is observed in YgjD while no nucleotide is bound on YeaZ. ITC experiments reveal previously unreported binary and ternary complexes which can be nucleotide dependent. The stoichiometry of the YeaZ-YgjD complex is 1:1 with a K(D) of 0.3 µM. YgjD and YjeE interact only in the presence of ATP, while YjeE binds to YgjD-YeaZ in the presence of ATP or ADP with a K(D) of 6 µM. YgjD doesn't bind the precursors of t⁶A, threonine, and bicarbonate. These results show a more complex set of interactions than previously thought, which may have a regulatory role. The understanding gained should help in deriving inhibitors of these essential proteins that might have potential as antibacterial drugs.


    Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE M22 PEPTIDASE YEAZ
A, D
231Salmonella typhimurium (strain 4/74)Mutation(s): 0 
Gene Names: yeaz
Find proteins for E8X8J1 (Salmonella typhimurium (strain 4/74))
Go to UniProtKB:  E8X8J1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
B, E
337Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: tsaD (gcp)
EC: 2.3.1.234
Find proteins for P40731 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P40731
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
B, E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
B, E
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.653 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.159 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.214α = 107.66
b = 68.084β = 92.63
c = 87.624γ = 116.45
Software Package:
Software NamePurpose
PHENIXrefinement
RESOLVEphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Database references
  • Version 1.2: 2017-03-29
    Type: Atomic model, Database references, Structure summary