5O5O

X-ray crystal structure of RapZ from Escherichia coli (P32 space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.404 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.

Gonzalez, G.M.Durica-Mitic, S.Hardwick, S.W.Moncrieffe, M.C.Resch, M.Neumann, P.Ficner, R.Gorke, B.Luisi, B.F.

(2017) Nucleic Acids Res. 45: 10845-10860

  • DOI: 10.1093/nar/gkx732
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory s ...

    In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory small RNA GlmZ to the essential ribonuclease RNase E for inactivation. Here, we report the crystal structures of full length Escherichia coli RapZ at 3.40 Å and 3.25 Å, and its isolated C-terminal domain at 1.17 Å resolution. The structural data confirm that the N-terminal domain of RapZ possesses a kinase fold, whereas the C-terminal domain bears closest homology to a subdomain of 6-phosphofructokinase, an important enzyme in the glycolytic pathway. RapZ self-associates into a domain swapped dimer of dimers, and in vivo data support the importance of quaternary structure in RNA-mediated regulation of target gene expression. Based on biochemical, structural and genetic data, we suggest a mechanism for binding and presentation by RapZ of GlmZ and the closely related decoy sRNA, GlmY. We discuss a scenario for the molecular evolution of RapZ through re-purpose of enzyme components from central metabolism.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNase adapter protein RapZ
A, B, C, D
284Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rapZ (yhbJ)
Find proteins for P0A894 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A894
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.404 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 92.750α = 90.00
b = 92.750β = 90.00
c = 156.800γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomRG84381
Austrian Science FundAustriaP 26681-B22
Austrian Science FundAustriaF4317

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Database references