5O5S

X-ray crystal structure of the RapZ C-terminal domain from Escherichia coli

Summary for 5O5S

• Entry DOI: 10.2210/pdb5o5s/pdb
• Descriptor: RNase adapter protein RapZ, MALONATE ION (3 entities in total)
• Functional Keywords: rna binding amino-sugar metabolism kinase like domain pfk like domain, chaperone
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 15552.74

Authors

Gonzalez, G.M.,Durica-Mitic, S.,Hardwick, S.W.,Moncrieffe, M.,Resch, M.,Neumann, P.,Ficner, R.,Gorke, B.,Luisi, B.F. (deposition date: 2017-06-02, release date: 2017-08-30, Last modification date: 2024-05-08)

Primary citation

Gonzalez, G.M.,Durica-Mitic, S.,Hardwick, S.W.,Moncrieffe, M.C.,Resch, M.,Neumann, P.,Ficner, R.,Gorke, B.,Luisi, B.F.
Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.
Nucleic Acids Res., 45:10845-10860, 2017

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.

PubMed: 28977623
DOI: 10.1093/nar/gkx732

Experimental method

X-RAY DIFFRACTION (1.17 Å)