5O5O

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.204 

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:  
    5O5S, 5O5O, 5O5Q

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNase adapter protein RapZA, B, C, D284Escherichia coliMutation(s): 0 
Gene Names: rapZ, yhbJ, b3205, JW3172
Find proteins for P0A894 (Escherichia coli (strain K12))
Explore P0A894 
Go to UniProtKB:  P0A894
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.204 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.75α = 90
b = 92.75β = 90
c = 156.8γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

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
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Database references