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

Experimental Data Snapshot

  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1093/nar/gkx732
  • Primary Citation of Related Structures:  
    5O5O, 5O5Q, 5O5S

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNase adapter protein RapZA,
C [auth D],
D [auth C]
295Escherichia coliMutation(s): 0 
Gene Names: rapZyhbJb3205JW3172
Find proteins for P0A894 (Escherichia coli (strain K12))
Explore P0A894 
Go to UniProtKB:  P0A894
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A894
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D],
R [auth C],
S [auth C]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.54α = 90
b = 91.54β = 90
c = 352.55γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • 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