4AM3: Crystal Structure Of C. Crescentus Pnpase Bound To Rna

Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3' end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a 'splayed' conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the alpha-proteobacteria.
PDB ID: 4AM3Download
MMDB ID: 98871
PDB Deposition Date: 2012/3/7
Updated in MMDB: 2012/07
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
Escherichia coli BL21(DE3)
Similar Structures:
Biological Unit for 4AM3: heptameric; determined by author and by software (PISA)
Molecular Components in 4AM3
Label Count Molecule
Proteins (3 molecules)
Polyribonucleotide Nucleotidyltransferase(Gene symbol: CC_0034)
Molecule annotation
Nucleotide(1 molecule)
RNA, 5'-r(*up*ap*ap*cp*up*up*up*gp*gp)-3'
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

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