SUPPLEMENTARY INFORMATION
Figure legends
Fig. S1. RNase E catalytic domain structure and sequence conservation. Structure
based sequence alignment of representative members of the RNase E/G family. The
multiple-sequence alignments are from Clustal W26 alignments of RNase E
Salmonella enterica (Q5PGV1), RNase E Yersinia pseudotuberculosis (Q669K5),
RNase E Yersinia pestis (Q8D0Q9), RNase E Haemophilus influenzae (P44443),
RNase E Vibrio cholerae (Q9KQG8), RNase E Xylella fastidiosa (Q9PAB1), RNase
E Neisseria meningitidis (Q9K1F8), RNase E Legionella pneumophila (Q5X2Z2),
RNase E Rickettsia prowazekii (Q9ZDR9), RNase E Rickettsia conorii (Q92IS8),
RNase E Escherichia coli (P21513) and RNase G Escherichia coli (P25537), but for
simplicity only the last two sequences are shown. The sequences are formatted with
ESPript27, highlighting the patterns of conservation. Grey highlighted residues are
totally conserved. 70% conserved residues are boxed in light grey. The sequences are
also annotated with the secondary structure of E. coli RNase E catalytic domain. The
secondary structure elements are colour coded with the same scheme as used in Fig. 2
in the main text. Strands are labelled 1-24 and helices are labelled a-n. Pi helices are
shown η1-5. Labels: () residues involved in the catalytic mechanism (F57, F67,
K112, D303, N305 & D346); () residues involved in 5’sensing (R169, T170 &
G124 form the 5' P recognition pocket and V128, I167, D183, W191, D220 & R371
support the pocket); () residues involved in the Zn-link; () residues involved in
making RNA contacts (R48 contacts phosphate +2 from scissile phosphate, K106
contacts base -1 and phosphate -2, R373 contacts phosphate at position 2 from 5’ end,
1
Q390 contacts phosphate -3, R391 contacts phosphate -1); triangles highlight residues
involved in domain contacts between two different protomers, () principal to
principal domain, () principal to small domain and () small to small domain
contacts; () residues forming H-bonds and salt-bridges (R15-E272, E210-R219,
D220-R371, D220-R219, D220-R169, R281-D294, D370-R389 bond within one
protomer), (R281-E297 through water molecule), (E13-R425, S267-E429, E276R414, S380-E386, H402-D415, N416-Y500, N453-R456, E454-main chain, E454S499 and R456-E463 bond between protomers). The key contacts between the small
domains, which organise the tetramer as a dimer of dimers are not conserved between
RNase E and RNase G. This may account for the observations that RNase G is a
homodimer28.
Figure S2
Structural decomposition of the catalytic domain of RNase E. (a) Linear
representation of the subdomain boundaries. (b) The isolated protomer and (c) its key
subdomains.
Figure S3
The superposition of RNase E complexes with 10, 13 and 15-mer RNAs. An overlay
of the complexes is shown in the top and the bottom panel shows the sequences with a
red asterisk (*) denoting the position located at the active site.
2