5O5Q

X-ray crystal structure of RapZ from Escherichia coli (P3221 space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 

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

    Georg-August University Göttingen, Department of Molecular Structural Biology Justus von Liebig Weg 11, D-37077 Göttingen, Germany.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.,Department of Microbiology, Immunology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNase adapter protein RapZ
A, B, D, C
295Escherichia 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: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.540α = 90.00
b = 91.540β = 90.00
c = 352.550γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

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