PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Cas4 Nuclease and Bacterial Immunity
February 2014
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Stabilizing DNA Single Strands
July 2013
AlkB Homologs
August 2012
Methyl maintenance
May 2012
Follow the RNA leader
December 2011
RNA Chaperone NMB1681
July 2011
Seeing HetR
July 2011
Structure from sequence
July 2011
Added benefits
April 2011
Nitrile Reductase QueF
March 2011
Inhibiting factor
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
tRNA Isopentenyltransferase MiaA
August 2010
Mre11 Nuclease
May 2010
Seek and destroy 8-oxoguanine
May 2010
Antibiotics and Ribosome Function
March 2010
Pseudouridine Synthase TruA
November 2009
Get3 into the groove
October 2009
Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1
October 2009
Proofreading RNA
July 2009
Hda and DNA Replication
June 2009
The elusive helicase
April 2009
Poly(A) RNA recognition
January 2009
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
RNase T
July 2008
SARS Coronavirus Nonstructural Protein 1
June 2008

Research Themes DNA and RNA

RNA Chaperone NMB1681

SBKB [doi:10.3942/psi_sgkb/fm_2011_7]
Featured System - July 2011
Short description: The small protein NMB1681 has been proposed to act as an RNA chaperone, but unlike a chaperone at a high school dance, NMB1681 acts as a molecular matchmaker, trying to bring together the molecules it watches over, rather than keeping them apart.

The small protein NMB1681 has been proposed to act as an RNA chaperone, but unlike a chaperone at a high school dance, NMB1681 acts as a molecular matchmaker, trying to bring together the molecules it watches over, rather than keeping them apart. RNA chaperones guide RNA molecules through their interactions, making sure that they meet their proper partners and don't get stuck in unproductive pairings. In the case of NMB1681, a small regulatory RNA and a messenger RNA are the molecules being chaperoned.

Chaperoning Duties

NMB1681 is thought to act like the similar RNA chaperone FinO. It performs several functions. First, it binds to a stem-loop structure in a small regulatory RNA, protecting it from degradation by cellular ribonuclease enzymes. Then, it pairs the small RNA with a complementary sequence in a messenger RNA, which also forms a distinctive stem-loop structure. The complex of the two RNA molecules hides the Shine-Delgarno sequence and thus reduces production of proteins from the message.

Structured and Unstructured

Both NMB1681 and FinO are composed of two parts, which perform different aspects of their function. The core of NMB1681, recently solved by MCSG researchers and shown here from PDB entry 3mw6, performs the first task, recognizing the stem-loop structure and protecting it. The rest of the protein forms an unstructured tail that is essential for the chaperoning task of bringing the two RNA molecules together. This type of unstructured protein is actually quite common in RNA chaperones, and may play a role in the process of folding and unfolding of RNA secondary structure like the stem-loop structures.

Complementary Charge

The NMB1681 has a distinctive shape and chemical composition. It is saddle-shaped, with a dense collection of arginine, lysine, and histidine amino acids (shown above in blue) on the curve of the saddle. These amino acids normally carry a positive charge, which is perfect for stabilizing the many negatively-charged phosphates on the RNA strands. Serendipitously, the crystal lattice in this structure solution includes six independent copies of the protein, so the structure also gives a glimpse at the essential flexibility of the protein. To see these structures, click on the lower image for an interactive Jmol.

The JSmol tab below displays an interactive JSmol

RBBP9 (PDB entry 2qs9)

RBBP9 binds to Rb and also has a serine protease active site. The distinctive LxCxE Rb-binding motif is colored green with the three sidechains in atomic colors. Notice that the leucine and cysteine are buried in the protein, so some rearrangement will probably be necessary when the RBBP9 binds to Rb. The catalytic triad in the active site, composed of a serine, histidine and aspartate, are also shown in atomic colors. Use the buttons to switch representations.

References

  1. Chaulk, S. et al. N. meningitidis 1681 is a member of the FinO family of RNA chaperones. RNA Biology 7, 812-819 (2010).

  2. Ghetu, A. F., Gubbins, M. J., Frost, L. S. & Glover, J. N. M. Crystal structure of the bacterial conjunction repressor FinO. Nature Structural Biology 7, 565-569 (2000).

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health