692.

Sobemovirus Peptidase 3141

Eric J. Snijder
Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, LUMC E4-P, PO Box 9600, 2300 RC Leiden,
The Netherlands. Email: e.j.snijder@lumc.nl

Alexander E. Gorbalenya
Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, LUMC E4-P, PO Box 9600, 2300 RC Leiden,
The Netherlands. Email: a.e.gorbalenya@lumc.nl

Handbook of Proteolytic Enzymes, 3rd Edn © 2013 Elsevier Ltd. All rights reserved.
ISBN: 978-0-12-382219-2 DOI: http://dx.doi.org/10.1016/B978-0-12-382219-2.00691-8

Chapter 692

Sobemovirus Peptidase

DATABANKS Genome Organization of Sobemoviruses

(+) g RNA
MEROPS name: sobemovirus peptidase ORF2b/RdRp
3⬘
MEROPS classification: clan PA, subclan PA(S), family 5⬘ ORF2a/Protease-VPg-p10-p8 ORF3/CP
VPg

S39, subfamily S39A, peptidase S39.001 ORF1/MP

Species distribution: superkingdom Viridae E132 E325 E402 E498

Reference sequence from: cocksfoot mottle virus Polyprotein 2a N Protease VPg P10 P8 C
S133 T326 T403 S499

E132 E325 E402

Polyprotein 2ab N Protease VPg RdRp C
Name and History S133 T326 T403

Sobemoviruses, named after their type member Southern
bean mosaic virus (SBMV), infect both monocots and
dicots [1]. These viruses are icosahedral with a diameter
of 30 nm and contain a genomic RNA (gRNA) of
approximate size 4
4.5 kb. The gRNA is covalently
attached at its 50 end to viral protein genome linked
(VPg) and lacks a poly A tail [1]. The gRNA encodes for
four overlapping ORFs; the 50 and 30 proximal ORFs
encode for movement protein (ORF1) and coat protein
(ORF 3), respectively (Figure 692.1). The central two
overlapping ORFs (ORF 2a and 2b) are translated into
polyproteins (2a and 2ab). The domain arrangements in
polyproteins 2a and 2ab are protease
VPg
p10
p8 and
protease
VPg
RdRp, respectively [2] (Figure 692.1).
The N-terminal protease and VPg are common to both 2a
and 2ab. However, expression of 2b (RdRp) is mediated
through a 21 ribosomal frame shifting mechanism
(Figure 692.1) [3,4]. The N-terminal protease is responsi-
ble for the processing of the polyproteins into functional
proteins and is called Sobemovirus peptidase. The
sequence of this peptidase contains the conserved
FIGURE 692.1 SeMV Genome Organization: SeMV is a single-
stranded RNA virus with genome size of 4149 nt. The 50 end of the
genome is covalently linked to VPg and the 30 end lacks polyA tail.
ORF 1 encodes movement protein and ORF 3 encodes coat protein. The
ORF 2 encodes for two polyproteins 2a/2ab. Polyprotein 2a and 2ab
have the domain arrangement shown in the figure.
catalytic triad present in cellular serine proteases [5,6].
Consensus catalytic triad residues are present in all the
sobemovirus peptidases [1]. The only other family of
plant viruses in which such conserved residues are present
in the protease domain of the polyproteins is the
Luteoviridae family. Interestingly, although the peptidase
contains the catalytic triad of serine proteases, its speci-
ficity is widely different. It has been predicted that the
Luteovirus and Sobemovirus polyproteins are cleaved at
(Gln, Glu)#(Gly, Ser, Thr, Ala) sites [6]. Much of the
information on structural and biochemical properties of
Sobemoviral peptidases has been obtained from studies
on the enzyme from Sesbania mosaic virus (SeMV).
Therefore, the following sections describe the properties
of SeMV protease.