3NBF

Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP

Summary for 3NBF

• Entry DOI: 10.2210/pdb3nbf/pdb
• Related: 3MWJ 3MWK 3MWL
• Descriptor: Heat resistant RNA dependent ATPase, [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate, [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate, ... (4 entities in total)
• Functional Keywords: rna helicase, ribosome biogenesis, atp hydrolysis, base specificity, thermostability, hydrolase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 4
• Total formula weight: 93124.62

Authors

Rudolph, M.G.,Klostermeier, D. (deposition date: 2010-06-03, release date: 2011-03-23, Last modification date: 2023-11-01)

Primary citation

Strohmeier, J.,Hertel, I.,Diederichsen, U.,Rudolph, M.G.,Klostermeier, D.
Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
Biol.Chem., 392:357-369, 2011

PubMed Abstract: DEAD-box proteins disrupt or remodel RNA and protein/RNA complexes at the expense of ATP. The catalytic core is composed of two flexibly connected RecA-like domains. The N-terminal domain contains most of the motifs involved in nucleotide binding and serves as a minimalistic model for helicase/nucleotide interactions. A single conserved glutamine in the so-called Q-motif has been suggested as a conformational sensor for the nucleotide state. To reprogram the Thermus thermophilus RNA helicase Hera for use of oxo-ATP instead of ATP and to investigate the sensor function of the Q-motif, we analyzed helicase activity of Hera Q28E. Crystal structures of the Hera N-terminal domain Q28E mutant (TthDEAD_Q28E) in apo- and ligand-bound forms show that Q28E does change specificity from adenine to 8-oxoadenine. However, significant structural changes accompany the Q28E mutation, which prevent the P-loop from adopting its catalytically active conformation and explain the lack of helicase activity of Hera_Q28E with either ATP or 8-oxo-ATP as energy sources. 8-Oxo-adenosine, 8-oxo-AMP, and 8-oxo-ADP weakly bind to TthDEAD_Q28E but in non-canonical modes. These results indicate that the Q-motif not only senses the nucleotide state of the helicase but could also stabilize a catalytically competent conformation of the P-loop and other helicase signature motifs.

PubMed: 21391900
DOI: 10.1515/BC.2011.034

Experimental method

X-RAY DIFFRACTION (1.9 Å)