Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 131306.03 
• Atom Count: 8240 
• Residue Count: 1136 
• Unique protein chains: 1

5O5O

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

• DOI: 10.2210/pdb5O5O/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2017-06-02 Released: 2017-08-30 
• Deposition Author(s): Gonzalez, G.M., Durica-Mitic, S., Hardwick, S.W., Moncrieffe, M., Resch, M., Neumann, P., Ficner, R., Gorke, B., Luisi, B.F.
• Funding Organization(s): Wellcome Trust; Austrian Science Fund 

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Experimental Data Snapshot

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

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

• PubMed: 28977623 
• DOI: 10.1093/nar/gkx732
• Primary Citation of Related Structures:  
  5O5S, 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
RNase adapter protein RapZ	A, B, C, D	284	Escherichia 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 92.750	α = 90.00
b = 92.750	β = 90.00
c = 156.800	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-02 
• Released Date: 2017-08-30 
• Deposition Author(s): Gonzalez, G.M., Durica-Mitic, S., Hardwick, S.W., Moncrieffe, M., Resch, M., Neumann, P., Ficner, R., Gorke, B., Luisi, B.F.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	RG84381
Austrian Science Fund	Austria	P 26681-B22
Austrian Science Fund	Austria	F4317

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