RNA Exosomes

What InterPro Tells Us

P46948 Yeast Exosome Rrp41 subunit

InterPro Domain Architecture

InterPro Entry	Signatures	Graphical Match	Method Name
IPR001247	PF01138		RNase_PH
IPR015847	PF03725		RNase_PH_C
IPR015847	SSF55666		3_ExoRNase
Structural Features
ModBase	MB_P46948

From the graphical match in the table above, you can see that the signatures are grouped into two InterPro entries for yeast Rrp41. These entries identify the domain architecture of this protein.

DOMAIN Entries

Ø IPR001247: Phosphorolytic domain 1 of exonuclease proteins, represented by one signature: PF01138 (PFAM).

Ø IPR015847: Phosphorolytic domain 2 of exonuclease proteins, represented by two signatures: PF03725 (PFAM) and SSF55666 (SUPERFAMILY).

Yeast exosome Rrp41 exonuclease has two PH domains, domain 1 having a 2-layer alpha/beta structure (similar to ribosomal protein S5) and domain 2 having a 3-layer alpha/beta/alpha structure. Both of these PH domains are also found in bacterial/organelle PNPases

Structural features

The remaining entry in the table above gives information on the predicted structure of this protein. This entry presents predicted structural data from the homology-modelling database ModBase. No known structural data exists for this particular protein, however there are known structures for PH domains from different PNPases useful as homology model templates. As shown above, the homology model from ModBase covers the entire protein.

What the Structure Tells Us

There are structures available for PNPases, archaeal and eukaryotic exosomes, as well as for various proteins containing PH, S1 and KH domains, in the Protein Data Bank (PDB). A detailed description and visualisation of the structural features of exosomes can be found at the PDB ‘Molecule of the Month’. The crystallographic structures of archaeal and eukaryotic exosomes have provided insight into their mode of RNA substrate binding and degradation.

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