Vol. 72, No. 1,1976
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
THE CRYSTAL STRUCTURE OF PENICILLOPEPSIN I-Nan
Hsu,
Theo Hofmann,
AT 6 i RESOLUTION
Stanley
C. Nyburg
Departments
of Biochemistry and Chemistry University of Toronto Toronto, Ontario. M5S lA8 and Michael
MRC Group
Received
July
N.G.
James
on Protein Structure and Function Department of Biochemistry University of Alberta Edmonton, Alberta. T6G 2H7
14,1976
SUMMARY: A 6 i resolution electron density map of crystals of penicillopepsin, an acid protease from Penicillium janthinellum,, has been computed from multiple isomorphous replacement phases determined from two heavy metal derivatives, K2PtC16 and U02C12. The mean figure of merit of the map is 0.939. The boundaries of the molecules, of which there are four per unit cell, are readily discgrnible& The yolecule is highly asymmetric with approximate dimensions 60 A x 40 A x 30 A. The molecule consists of two distinct lobes separated by a deep cleft, which is probably the extended substrate binding site. Penicillopepsin mould acid
is an extracellular
Penicillium
janthinellum.
proteases
specificity on the
in amino
catalytic
and porcine
sequence
of fragments
evidence
that
hoped will
that provide
pepsin
of action
pepsin
more compelling
should
of the acid
of which provide
has been further
for
by the and other
pH-optimum, Recent
similarity
studies between
A comparison
of the primary
with
pepsin
porcine
homologues
of the tertiary
proteases.
(l-3).
evolutionary
evidence
pepsin weight,
a striking
of penicillopepsin
the determination
it
inhibitors
(4).
produced
porcine
molecular
revealed
the two enzymes are
the structure
In addition,
covalent
have
protease
resembles
composition,
with
mechanism
penicillopepsin
It
acid
and reaction
acid
structure
(5). at high
the evolutionary
determined insight
provides It
is
resolution
homology
with
to 2.7 5; resolution into
the
As an intermediary
step
complex
(6).
mechanism
towards
a high n
resolution
Copyright All rights
structure
0 I976 by Academic Prms, of reproduction itz any form
of penicillopepsin
Inc. resewed.
we report 363
the
results
of a 6 A
Vol. 72, No. 1, 1976
resolution data
BIOCHEMICAL
X-ray
have already
other
fungal
chinensis
(9)
work
b = 46.6
Heavy-atom
derivatives
atom solutions
up-take
one week for
used
parasitica
(8)
of two
and Rhizopus
grown
as described
(7),
of 2.5 M (NH4)2SO4.
The rhombic
dimensions
a = 97.4
1,
8 = 115.4
(2),
group
were
prepared
of heavy
space
by soaking
2.5 M Li2S04
(2) i, C2.
crystals
at pH = 4.4.
atoms was two weeks
that
in 0.1 M sodium
cell
(1)
except
for
in heavy-
The soaking
time
1 mM K2PtC16
and
1 mM U02C12.
A Picker the
instead
made up with
for
Endothia
structures
used was 2.5 M Li2S04
are monoclinic, c = 65.4
Low resolution
were
the solvent
(1) i,
required
from
crystallographic
been published.
pH = 4.4,
crystals
Preliminary
(7).
of penicillopepsin
buffer,
prismatic
proteinases
have recently
in the present acetate
determination.
been published
acid
Crystals
for
structure
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
FACS-1 diffractometer,
diffracted
modified
beam collimator
to collect
the
intensity
by an extended
(crystal
data
to counter
(hk!& and Friedel
helium
distance
path
65 cm) was
mate hcE) within
the
n
6 A sphere.
The incident
was 8128 with Individual 10 set three
standard
intensity With
such a small from
A total
values
three
reflections
apparent
X-ray crystal
of 1356 reflections
was 0.037 for
spectively. amplitudes
for
measured
every
a single
The agreement
were
CuKol.
scan width at both
damage due to X-irradiation
reflections
of these
collected
counts
Crystal
was Ni-filtered
of 2' min -1 , the
a scan speed
background each.
radiation
were
indices
the reflections
the K2PtC16
between from
and uranyl
The agreement
indices
the native derivatives for
the
by remeasuring
set
range of data
each of the three
pairs
(C 1 I+ - I-
of
of data. could
be
were scaled
crystals.
( / C)
The corresponding
crystal. 0.124 structure
(C 11 FpH 1 - 1 Fp ( 1 / C 1 Fp I) between
364
for
enzyme and each derivative. from
Bijvoet
in 28.
of the scan
the whole
complete
native
collected
limits
1.5"
The maximum variation
was 4% over
of the
being
was monitored
50 reflections.
damage the
The scan mode
and 0.104
re-
factor
the two derivatives
Vol. 72, No. 1, 1976
(K2PtC16
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
and IJO2C12) and the native
crystals
was 0.221
and 0.163
re-
spectively. Three
dimensional
terms
of one major
Their
y-coordinates
difference platinum were
of these
phased
maps (11).
Protein morphous tering
phases
phase data
further heavy-atom
Refinement
data
is
satisfactorily the phase
over
some four the whole
Residual
given
for
1.
both
given
in Table
3.
small
and give
an important
times
higher
than
It
is the
cross-
configuration
summarized
derivatives
the r.m.s.
r.m.s.
IfHI‘s
errors,
lEH[
e-range.
TABLE 1 Heavy atom coordinates
(x104),
and temperature Derivative
relative
factors
occupancies,
A,
B(i2)
Site
x
Y
z
A
B
PtCl;-
1 2 3
571 473 598
(0) 959 165
169 48 83
28.0 10.9 8.4
43 43 43
UO;
1 2 3 4
286 738 337 628
565 715 777 908
239 428 347 348
14.4 8.2 9.4 3.5
29 29 29 29
365
in anoare
of the accuracy
that
corresponding
of merit
from the
both
two
refined
figure are
indication
scat-
revealed The
derivatives
noteworthy
iso-
dispersion
site.
for
(10).
by multiple
The overall
The R factors
sites.
function
syntheses
uranyl
of the absolute
(13).
binding
data
Fourier
in Table
in
by calculating
heavy atom anomalous
statistics
determination
interpreted
uranyl
from derivative
and one minor
2 and the determination
malous
are
(12).
are
and three
was verified
in which
sites
maps were
by the use of Rossmann's
calculated
included
parameters
was 0.939. Table
were
platinum
site
coordinates
refinement
were
minor
binding assigned
The assignment Fourier
Patterson
of
BIOCHEMICAL
Vol. 72, No. 1,1976
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
TABLE 2 Phase
refinement
+2
PtC16=
Derivative
Rk (all) Rk (centric) R, (all> Rc (centric) r.m.s. I fH I r.m.s. EH
\
statistics
"O2
0.060 0.088 0.255 0.260 60.86 14.39
0.037 0.057 0.249 0.259 39.41 9.12
= c 1 FpH - 1 Fp + fH 1 1 / c FpH =
RC
CIIFpH
-
Fp\
-
fHI/CIFpH-Fpl
amplitudes where FP, FPU and fH are structural lEHl derivative and heavy atom, respectively. error in the phase triangles.
for native protein, is the lack of closure
TABLE 3 Determination Anomalous Included Included
Data
The electron (14) In most molecule approximate similar
r.m.s.E
14.32 19.44
areas
resembles
to those
with
perpendicular
boundaries
an elongated
and slightly
reported
\(")
10.68 14.14
0.060 0.081
0.037 0.058
the
use of the final
to the y-axis
the molecular
dimensions
Rk(W
U
m* 0.939 0.902
of merit
map was calculated
in sections
configuration
r.m.s.Ept
correctly incorrectly
* m is mean figure
phases
of absolute
were
the acid
366
clearly
about
ellipsoid
These
dimensions
proteinases
2 i apart.
defined.
flattened
of 60 i x 40 i x 30 i. for
spaced
708 "best"
of Endothia
The with
the
are very (8)
and
BIOCHEMICAL
Vol. 72, No. 1, 1976
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Electron density map at Fig. 1. Sections parallel to the b axis. The tween y = 0.10 and y = 0.40. is at the bottom of this drawing
Rhizopus
(9)
and those
maps representing
of pig
6 i resolution viewed in a direction are calculated at 0.05 intervals becleft which comprises the active site of the map.
pepsin
one molecule.
(6).
A deep
Fig.
1 shows electron
groove
running
density
parallel
to the
n
40 A axis ported
(b-axis)
for
(9).
hibitors
are
site, with
In the located
the groove
sumably
clearly
the Endothia
protease
that
is
evidence
for
groove
divides
is
case it
pig
pepsin
It
is
contains
T.T.
(15)
therefore
recently
analogous
to that
proposed
the molecule
into
two distinct
T., for
and the Rhizopus
site.
pre-
hydrophobic
binding
from kinetic
studies
pepsin
compact
in-
to assume It
unpublished). pig
site
reasonable
the active
& Hofmann,
have been re-
two active
of the extended
has been obtained
(Wang,
grooves
was shown that
the location
which
substrates
site
latter
(8),
in penicillopepsin
represents
binding
protease
Similar
in the groove.
also
small
visible.
This (16,
globular
17).
The
regions.
Acknowledgements We wish
to thank
Mrs.
Anne DeJong
367
for
her
able
technical
assistance,
Vol. 72, No. 1,1976
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Mr. Peter Dalziel, Dr. Pei-Tak Cheng and Miss Dorothy Dangelat for the earlier photographic work, Dr. Louis T.J. Delbsere for his invaluable assistance in collecting and processing the 6 A data, Dr. Wendy L.B. Hutcheon for using her computer programs, and Professor R.E. Dickerson for providing us with a copy of his phase determination program. This work has been supported by a grant from the Medical Research Council of Canada, MRC MA-2438.
References 1.
2. 3. 4. 5. 6.
Sodek, J., and Hofmann, T. (1971) Meth. Enzymol. 19, 372-396. Mains, G., Takahashi, M., Sodek, J., and Hofmann, T. (1971) Can. J. Biochem. 49, 1134-1149. Mains, G., and Hofmann, T. (1974) Can. J. Biochem. 52, 1018-1023. Takahashi, M., and Hofmann, T. (1975) Biochem. J. 147, 549-563. Cunningham, A., Wang, H.-M., Jones, S.R., Kurosky, A., Rao, L., Harris, C.I., Rhee, S.-H. and Hofmann, T. (1976) Can. J. Biochem. (in press). Andreeva, N.S., Fedorov, A.A., Gushina, A.E., Shutskever, N.E., Riskulov, R.R., and Vol'nova, T.V. (1976) Dokl. Akad. Nauk. SSSR,
228, 480. 7.
8. 9. 10. 11. 12.
13. 14.
15. 16. 17.
Camerman, N., Hofmann, T., Jones, S., and Nyburg, S.C. (1969) J. Mol. Biol. 44, 569-570. Jenkins, J.A., Blundell, T.L., Tickle, I.J., and Ungaretti, L. (1975) J. Mol. Biol. 99, 583-590. Subramanian, E., Swan, I.D.A., and Davies, D.R. (1976) Biochem. Biophys. Res. Commun. 68, 875-880. Stewart, J.M., Kundall, F.A., and Baldwin, J.C. (1970) X-Ray 70 System, University of Maryland, College Park, Maryland. 13, 221-226. Rossmann, M.G. (1960) Acta Cryst., Matthews, B.W. (1966) Acta Cryst., 20, 82-86. J.E. and Palmer, R.A. (1968) Acta Cryst., Dickerson, R.E., Weinzierl, B24, 997-1003. Blow, D.M., and Crick, F.H.C. (1959) Acta Cryst., 12, 794-802. Andreeva, N.S., Borisov, U.U., Melik-Adamyan, U.R., Raiz, V.S., Trofimova, L.N., and Shutskever, N.E. (1971) Moleku. Biol. (USSR) 5, 908-916 (Engl. Transl. 5, 731). Fruton, J.S. (1970) Adv. Enzymol., 33, 401-443. and Hofmann, T. (1976) Biochem. J. 153, 691-699. Wang, T.T.,
368
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
THE CRYSTAL STRUCTURE OF PENICILLOPEPSIN I-Nan
Hsu,
Theo Hofmann,
AT 6 i RESOLUTION
Stanley
C. Nyburg
Departments
of Biochemistry and Chemistry University of Toronto Toronto, Ontario. M5S lA8 and Michael
MRC Group
Received
July
N.G.
James
on Protein Structure and Function Department of Biochemistry University of Alberta Edmonton, Alberta. T6G 2H7
14,1976
SUMMARY: A 6 i resolution electron density map of crystals of penicillopepsin, an acid protease from Penicillium janthinellum,, has been computed from multiple isomorphous replacement phases determined from two heavy metal derivatives, K2PtC16 and U02C12. The mean figure of merit of the map is 0.939. The boundaries of the molecules, of which there are four per unit cell, are readily discgrnible& The yolecule is highly asymmetric with approximate dimensions 60 A x 40 A x 30 A. The molecule consists of two distinct lobes separated by a deep cleft, which is probably the extended substrate binding site. Penicillopepsin mould acid
is an extracellular
Penicillium
janthinellum.
proteases
specificity on the
in amino
catalytic
and porcine
sequence
of fragments
evidence
that
hoped will
that provide
pepsin
of action
pepsin
more compelling
should
of the acid
of which provide
has been further
for
by the and other
pH-optimum, Recent
similarity
studies between
A comparison
of the primary
with
pepsin
porcine
homologues
of the tertiary
proteases.
(l-3).
evolutionary
evidence
pepsin weight,
a striking
of penicillopepsin
the determination
it
inhibitors
(4).
produced
porcine
molecular
revealed
the two enzymes are
the structure
In addition,
covalent
have
protease
resembles
composition,
with
mechanism
penicillopepsin
It
acid
and reaction
acid
structure
(5). at high
the evolutionary
determined insight
provides It
is
resolution
homology
with
to 2.7 5; resolution into
the
As an intermediary
step
complex
(6).
mechanism
towards
a high n
resolution
Copyright All rights
structure
0 I976 by Academic Prms, of reproduction itz any form
of penicillopepsin
Inc. resewed.
we report 363
the
results
of a 6 A
Vol. 72, No. 1, 1976
resolution data
BIOCHEMICAL
X-ray
have already
other
fungal
chinensis
(9)
work
b = 46.6
Heavy-atom
derivatives
atom solutions
up-take
one week for
used
parasitica
(8)
of two
and Rhizopus
grown
as described
(7),
of 2.5 M (NH4)2SO4.
The rhombic
dimensions
a = 97.4
1,
8 = 115.4
(2),
group
were
prepared
of heavy
space
by soaking
2.5 M Li2S04
(2) i, C2.
crystals
at pH = 4.4.
atoms was two weeks
that
in 0.1 M sodium
cell
(1)
except
for
in heavy-
The soaking
time
1 mM K2PtC16
and
1 mM U02C12.
A Picker the
instead
made up with
for
Endothia
structures
used was 2.5 M Li2S04
are monoclinic, c = 65.4
Low resolution
were
the solvent
(1) i,
required
from
crystallographic
been published.
pH = 4.4,
crystals
Preliminary
(7).
of penicillopepsin
buffer,
prismatic
proteinases
have recently
in the present acetate
determination.
been published
acid
Crystals
for
structure
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
FACS-1 diffractometer,
diffracted
modified
beam collimator
to collect
the
intensity
by an extended
(crystal
data
to counter
(hk!& and Friedel
helium
distance
path
65 cm) was
mate hcE) within
the
n
6 A sphere.
The incident
was 8128 with Individual 10 set three
standard
intensity With
such a small from
A total
values
three
reflections
apparent
X-ray crystal
of 1356 reflections
was 0.037 for
spectively. amplitudes
for
measured
every
a single
The agreement
were
CuKol.
scan width at both
damage due to X-irradiation
reflections
of these
collected
counts
Crystal
was Ni-filtered
of 2' min -1 , the
a scan speed
background each.
radiation
were
indices
the reflections
the K2PtC16
between from
and uranyl
The agreement
indices
the native derivatives for
the
by remeasuring
set
range of data
each of the three
pairs
(C 1 I+ - I-
of
of data. could
be
were scaled
crystals.
( / C)
The corresponding
crystal. 0.124 structure
(C 11 FpH 1 - 1 Fp ( 1 / C 1 Fp I) between
364
for
enzyme and each derivative. from
Bijvoet
in 28.
of the scan
the whole
complete
native
collected
limits
1.5"
The maximum variation
was 4% over
of the
being
was monitored
50 reflections.
damage the
The scan mode
and 0.104
re-
factor
the two derivatives
Vol. 72, No. 1, 1976
(K2PtC16
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
and IJO2C12) and the native
crystals
was 0.221
and 0.163
re-
spectively. Three
dimensional
terms
of one major
Their
y-coordinates
difference platinum were
of these
phased
maps (11).
Protein morphous tering
phases
phase data
further heavy-atom
Refinement
data
is
satisfactorily the phase
over
some four the whole
Residual
given
for
1.
both
given
in Table
3.
small
and give
an important
times
higher
than
It
is the
cross-
configuration
summarized
derivatives
the r.m.s.
r.m.s.
IfHI‘s
errors,
lEH[
e-range.
TABLE 1 Heavy atom coordinates
(x104),
and temperature Derivative
relative
factors
occupancies,
A,
B(i2)
Site
x
Y
z
A
B
PtCl;-
1 2 3
571 473 598
(0) 959 165
169 48 83
28.0 10.9 8.4
43 43 43
UO;
1 2 3 4
286 738 337 628
565 715 777 908
239 428 347 348
14.4 8.2 9.4 3.5
29 29 29 29
365
in anoare
of the accuracy
that
corresponding
of merit
from the
both
two
refined
figure are
indication
scat-
revealed The
derivatives
noteworthy
iso-
dispersion
site.
for
(10).
by multiple
The overall
The R factors
sites.
function
syntheses
uranyl
of the absolute
(13).
binding
data
Fourier
in Table
in
by calculating
heavy atom anomalous
statistics
determination
interpreted
uranyl
from derivative
and one minor
2 and the determination
malous
are
(12).
are
and three
was verified
in which
sites
maps were
by the use of Rossmann's
calculated
included
parameters
was 0.939. Table
were
platinum
site
coordinates
refinement
were
minor
binding assigned
The assignment Fourier
Patterson
of
BIOCHEMICAL
Vol. 72, No. 1,1976
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
TABLE 2 Phase
refinement
+2
PtC16=
Derivative
Rk (all) Rk (centric) R, (all> Rc (centric) r.m.s. I fH I r.m.s. EH
\
statistics
"O2
0.060 0.088 0.255 0.260 60.86 14.39
0.037 0.057 0.249 0.259 39.41 9.12
= c 1 FpH - 1 Fp + fH 1 1 / c FpH =
RC
CIIFpH
-
Fp\
-
fHI/CIFpH-Fpl
amplitudes where FP, FPU and fH are structural lEHl derivative and heavy atom, respectively. error in the phase triangles.
for native protein, is the lack of closure
TABLE 3 Determination Anomalous Included Included
Data
The electron (14) In most molecule approximate similar
r.m.s.E
14.32 19.44
areas
resembles
to those
with
perpendicular
boundaries
an elongated
and slightly
reported
\(")
10.68 14.14
0.060 0.081
0.037 0.058
the
use of the final
to the y-axis
the molecular
dimensions
Rk(W
U
m* 0.939 0.902
of merit
map was calculated
in sections
configuration
r.m.s.Ept
correctly incorrectly
* m is mean figure
phases
of absolute
were
the acid
366
clearly
about
ellipsoid
These
dimensions
proteinases
2 i apart.
defined.
flattened
of 60 i x 40 i x 30 i. for
spaced
708 "best"
of Endothia
The with
the
are very (8)
and
BIOCHEMICAL
Vol. 72, No. 1, 1976
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Electron density map at Fig. 1. Sections parallel to the b axis. The tween y = 0.10 and y = 0.40. is at the bottom of this drawing
Rhizopus
(9)
and those
maps representing
of pig
6 i resolution viewed in a direction are calculated at 0.05 intervals becleft which comprises the active site of the map.
pepsin
one molecule.
(6).
A deep
Fig.
1 shows electron
groove
running
density
parallel
to the
n
40 A axis ported
(b-axis)
for
(9).
hibitors
are
site, with
In the located
the groove
sumably
clearly
the Endothia
protease
that
is
evidence
for
groove
divides
is
case it
pig
pepsin
It
is
contains
T.T.
(15)
therefore
recently
analogous
to that
proposed
the molecule
into
two distinct
T., for
and the Rhizopus
site.
pre-
hydrophobic
binding
from kinetic
studies
pepsin
compact
in-
to assume It
unpublished). pig
site
reasonable
the active
& Hofmann,
have been re-
two active
of the extended
has been obtained
(Wang,
grooves
was shown that
the location
which
substrates
site
latter
(8),
in penicillopepsin
represents
binding
protease
Similar
in the groove.
also
small
visible.
This (16,
globular
17).
The
regions.
Acknowledgements We wish
to thank
Mrs.
Anne DeJong
367
for
her
able
technical
assistance,
Vol. 72, No. 1,1976
BIOCHEMICAL
AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Mr. Peter Dalziel, Dr. Pei-Tak Cheng and Miss Dorothy Dangelat for the earlier photographic work, Dr. Louis T.J. Delbsere for his invaluable assistance in collecting and processing the 6 A data, Dr. Wendy L.B. Hutcheon for using her computer programs, and Professor R.E. Dickerson for providing us with a copy of his phase determination program. This work has been supported by a grant from the Medical Research Council of Canada, MRC MA-2438.
References 1.
2. 3. 4. 5. 6.
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