BIOCHEMICAL
Vol. 63, No. 4,197s
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
ALPHA-CARBON COORDINATES FOR BOVINE CU,ZN SUPEROXIDE DISMUTASE Jane S. Richardson?, Kenneth A. Thomas*, and David C. Richardson* * Department of Biochemistry and +Department of Anatomy, Duke University, Durham, North Carolina 27710. Received
February
26,1975
Summary Preliminary a-carbon and metal coordinates are given for a subunit of the bovine erythrocyte Cutt,Zntt superoxide dismutase. The coordinates are avera ed from 5 sets of measurements made on electron density maps at 3 fi resolution: one set from an averaged map and one set from each of the 4 crystallographically independent subunits (2 dimeric molecules) in the asymmetric unit of the crystal. The 3-dimensional structure of the polypeptide backbone is illustrated and briefly described. The methods graphic
investigation
3x resolution the
listed
here
for
the
or approximate
Bovine C2, with
Cu,Zn
4 subunits
resolution
the
and
map for
zinc each
transforming, the
from
4 subunits.
averaged
map.
a common Cartesian
coordinate
of the
the
Copyright All righrs
dimer
along
per
o I9 75 by Academic Press. Inc. of reproduction in any form reserved.
y axis.
work
of
will
libe con-
coordinates
to
from
are models,
of
5 coordinate with
The 5 sets
space At
group 31
be identical
for
e-carbon,
cop-
the
An averaged
986
unit.
subunits.
measured
system
in
asymmetric appears
and a set All
to
metal
to make backbone
and averaging
calculation,
and the
crystallizes
independent
interpolating,
Fourier the
the
dismutase The course
a-carbon
dismutase
were
crystallo-
calculations.
conformation
coordinates of
traced
wishing
(2 molecules)
backbone
(1).
crystallographic
distance
4 crystallographically
per,
has been
anyone
superoxide
x-ray
superoxide
preliminary
use of
the
elsewhere
the
resolution,
of
Cutt,Zntt
chain
Although
to higher
results
described
backbone
tinued
of
been
identifisd.
drawings,
general
of bovine
have
polypeptide
gands
all
and the
electron
density
map was calculated the
numerical
coordinates sets
were
the
local
were
by
output
was measured transformed twofold
averaged,and
to axis dis-
Vol. 63, No. 4,1975
X
Ala Thr Lys Ala Val Cysh Val Leu Lys Gly Asp Gly Pro Val Gln Gly Thr Ile His Phe Glu Ala Lvs Giy Asp Thr Val Val Val Thr Gly Ser Ile Ti-ir Gly Leu Thr Glu Gly Asp His Gly Phe His Val His Glu Phe Gly Asp
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
cu
8.1 9.1 8.9 6.8 5.7 3.3 2.5 0.5 -0.9 -3.7 -6.3 -5.0 -2.6 -1.2 1.7 ?: 5.2 7.0 6.1 8.0 8.1 9.2 7.6 4.2 4.3 3.8 5.6 5.0 6.7 6.6 5.9 3.3 2.9 0.1 -2.1 -4.7 -4.2 -4.2 -5.6 -6.1 -6.7 -5.8 -6.9 -6.5 -8.9 -9.9 -8.8 -6.8 -8.0 --10.4
BIOCHEMICAL
Y -13.8 -12.7 -8.6 -5.5 -2.2 0.0
z 4.1 6.7 6.7 7.0 5.7 6.8 6.2
8.4 11.2 13.8 15.4 15.3 12.1 9.8 6.8 4.2 0.6 -2.3 -5.8 -9.3 -12.8 -14.6 -17.6 -18.1 -15.1 -11.8 -8.9 -5.4 -2.5 1.0 4.4 6.8 10.8 13.4 12.8 13.0 12.0 9.0 6.4 4.8 2.5 -0.2 -2.2 -3.9 -3.9 -6.1 -4.4 -2.5 0.1
2; Z:i 8.3 11.0 11.2 10.6 10.3 10.5 10.6 11.4 11.0 11.8 11.5 14.0 14.3 15.5 16.9 15.1 16.3 16.1 15.9 15.7 15.6 15.5 15.4 15.1 18.0 20.2 23.8 23.9 23.1 20.0 17.8 16.1 14.5 11.1 7.9 4.9 2.3 0.9 -1.3
-0.6
13.2
AND BIOPHYSICAL
X
Asn Thr Gin Gly cys Thr Ser Ala G1y Pro His Phe Asn Pro Leu Ser Lys Lys His Glv Gl; Pro Lys Asp Glu Glu Arg His Val Gly Asp Leu Gly Asn Val Thr Ala Asp Lys Asn Gly Val Ala Ile Val Aso 11; Val Asp Pro
51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Zn
-7.1 -9.6 -12.2 -10.1 -9.4 -12.7 -12.4 -11.1 -13.1 -13.8 -12.4 -10.6 -12.1 -12.1 -13.8 -16.5 -16.2 -16.7 -14.8 -12.6 -9.5 -6.1 -6.2 -9.5 -11.3 -13.1 -10.9 -10.9 -8.0 -7.6 -7.6 -5.4 -5.4 -4.7 -2.3 -1.1 -0.3 2.0 1.7 3.4 2.4 3.4 3.3 4.8 4.5 4.4 2.9 3.1 0.5 -0.5
RESEARCH COMMUNICATIONS
z Y 3.5 -1.5 4.8 -3.2 6.0 -1.4 7.0 1.0 5.3 3.9 4.8 3.4 2.1 1.7 0.0 3.5 -1.9 5.2 -3.8 7.5 -5.6 10.1 -9.0 9.8 -11.2 10.7 -13.9 9.7 -16.6.10.9 -14.9 12.0 -13.3 14.9 -10.6 17.3 -8.0 18.8 -8.1 20.7 -7.6 22.1 -8.4 21.7 -11.3 23.4 -12.8 23.8 -15.6 22.5 -13.5 20.9 -12.1 19.0 -10.8 15.9 -11.0 13.5 -8.0 13.4 -6.8 16.3 -5.6 17.8 -2.6 20.0 0.3 21.6 2.5 21.2 5.0 23.6 8.6 23.2 12.4 23.9 15.9 24.3 16.7 22.0 13.8 19.8 10.6 19.7 6.6 19.8 3.4 20.4 0.2 18.9 -2.8 20.8 -6.0 19.9 -9.9 20.0 -11.4 18.4 -14.5 18.0
-12.2
-5.7
Leu Ile Ser Leu Se?? Gly Glu Tyr Ser Ile Ile Gly Arg Thr Met Val Val His Glu Lys Pro Asp Asp Leu Gly Arg Gly Gly Asn Glu Glu Ser Thr Lys Thr Gly Asn Ala Gly Ser Arg Leu Ala cys Giy Val Ile Gly Ile Ala Lys
15.4
101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151
x -2.0 -1.2 0.0 1.9 1.6 -1.0 -4.4 -3.6 -2.2 -2.0 -0.9 -2.7 -4.1 -4.9 -3.7 -5.6 -5.6 -8.6 -9.8 -10.8 -10.3 -11.1 -13.2 -12.0 -15.1 -17.5 -19.2 -23.3 -23.6 -23.9 -20.7 -19.0 -19.4 -18.3 -16.0 -15.2 -16.0 -13.1 -14.0 -12.9 -10.4 -7.2 -4.4 -3.9 -2.2 -1.1 0.8 3.6 6.2 9.9 13.6
Y -14.9 -13.3 -14.7 -13.6 -16.4 -17.6 -17.6 -15.2 -12.6 -9.2 -8.2 -6.2 -5.0 -2.4 -0.9 1.3 4.2 5.6 8.4 6.9 4.6 1.2 -0.8 -3.9 -5.6 -4.9 -2.1 -2.5 -1.7 -2.7 -1.2 -3.3 -5.7 -4.4 -1.8 -0.1 2.7 3.6 5.7 7.1 6.8 8.5 7.2 4.8 2.6 -0.3 -3.3 -4.6 -6.8 -6.5 -7.0
Table I - Averaged a-carbon and metal coordinates for a subunit bovine Cu,Zn superoxide dismutase. Coordinates are orthogonal in 8. The t ransformation to obtain coordinates for the second subunit of a dimer molecule is: x1=-x, y'xy, z'=-z. crepancies
were
maps.
The root
dinate
sets
tween
0.8
reexamined mean square
and the and 0.9x.
on the
individual
errors
between
averaged No attempt
coordinates has been
987
electron the given
individual in
Table
made to refine
z 15.3 12.8 9.8 7.2 5.2 4.3 5.3 7.5 5.9 6.4 3.2 1.4 3.8 5.7 8.7 10.8 13.0 14.9 17.3 20.1 22.0 22.0 24.0 23.7 23.6 25.8 25.6 25.4 22.3 18.9 18.3 19.7 18.2 15.4 16.7 19.2 19.2 17.6 15.2 13.0 11.1 10.5 9.6 7.2 5.4 3.0 4.1 2.8 2.2 3.6 3.5
of and
density coorI are
be-
these
co-
Vol. 63, No. 4,1975
dihedral
bend
angle
angle
Ala
1
Thr
2
Lys
3
Ala
4
Val
5
Cysh
6
Val
7
Leu
8
Lys
9
Gly
10
Asp
11
Gly
12
(1800) 00 7E"
Val
14
Gln
15
Gly
16
Thr
17
Ile
18
His
19
123'= 288"
Glu
21
Ala
22
Gly
24
Asp
25
300 500
400
324O 1190
460 28O
161°
20
1970 185O 1770 284O 1200
85O 360 700 310 23O
3470
140
1300
450
326" 152O 3330 164O 190 164O
Lys 23
700
440
1170
Phe 20
(710)
330
3060
Pro 13
BIOCHEMICAL
910
390 500 46'= 330 61'= 65O 540
730
900
Ca-Ccc dist.
or to
Table carbons,
3.1 4.0 3.8 3.7 3.4 3.6 3.2 3.3 4.0 3.6
oxide
3.6 3.5 3.7 3.4 3.5 3.6
26
Val
21
Val
28
Val
29
Thr
30
Gly
31
Ser
32
Ile
33
Thr
34
Gly
35
Thr
37
Glu
38
Gly
39
Asp
40
His
41
Gly
42
3.5 3.7 4.1 3.5 3.3
His
44
Val
45
His
46
Glu
47
40 2090
3.5 3.6
Gly
49
Asp
50
62O
390
2410
32O
246O 242'= 62'= 237O 2940
90 350 42O 42O 750
1170 324O 247O 2010 266'= 63O 356" 161'= 288"
190 62O 710 330 48'= 200 28O 38" 370
1740 220 269O 298O 163O 298O
510 400 770 26" 590 510
dihedral angle
3.3 3.8 3.6 3.6 3.4 3.5 3.5 3.5 4.0 3.9 3.7 3.4
Asn
51
Thr
52
Gln
53
Gly
54
cys
55
Thr
56
Ser
57
Ala
58
Gly
59
Pro
60
His
61
Phe 62
3.8
Asn 63
2.9
1350
Leu 65
3.5
Ser 66
3.3
Lys
3.2
67
Lys 68
2.8 3.8 4.0 3.8 3.3 3.2
His
69
Gly
70
Gly
71
Pro
72
Lys
73
Glu
64O
262O
880
16S" 126O 217O
550 1040
2790 90 208" 206O 1220 18" 164O 3410 16O 2970 730 3300 261° 220 3190 233O 253O 10
Asp 74
3.6
7E"
226O
Pro 64
3.1
Ca-Ca
bend dist. angle R
251°
75
830 710 6S" 26O 390 56O 65O 52O 52'= 83O 62O 220 410 490 210 350 83O 6LI" 420 930
3.6 3.3 3.4 3.3 3.4 3.4 3.1 3.1 3.2 3.2 3.5 3.8 2.9 2.9 3.3 3.3 3.4 3.6 3.5 3.0 3.4 3.5 3.4 3.7 3.5
angles and a-carbon to cl-carbon distances a wire backbone model (2) of the bovine Cu,Zn Such a model is shown in Fig. 4. subunit.
adjust
them
these
Table
530
470
61°
Phe 48
RESEARCH COMMUNICATIONS
ca-ca bend dist. angle 1
1510
Phe 43
copper,
dismutase;
Thr
Leu 36
3.2
I lists the
dihed??a1 angle
8
Table II - The bend needed to construct superoxide dismutase
ordinates
AND BIOPHYSICAL
to
give
averaged
and the II
lists
standard
Ca-Ccr distances.
coordinates
zinc
of the 988
one subunit bend
angles,
for
the of
151 ccCu,Zn
dihedral
superangles,
Vol. 63, No. 4,1975
dihedFdl angle
Arg
77
His
78
Val
79
Gly
80
Asp
81
990 3150 1980 248O 0* 1360
Leu 82 Gly
10
83
5*
Ash 84 Val
85
Thr
86
Ala
87
Asp
88
Lys
83
2060 120 2910 146O 250 60°
Asn 90 Gly
91
Val
92
Ala
93
Ile
94
Val
95
Asp
96
Ile
97
Val
98
338O 1060 312O 164O 220 1770 322O 142O 32Ei"
Asp 33 Pro
100
1770
3.2
780
Ile
3.3
560
Gly
2.9
480
Tyr
3.5
490
3.7
490
3.1
250
4.5
36O
3.6
83O
3.0
85O
3.4
200
4.1
27O
3.6
46O
3.5
58O
111
Gly
112
Arg
113
Thr
114
203O 226O 34E" 252O 920
Val
116
Val
117
His
118
Glu
119
306O 1280 3100 1920 226O 1470 340 237O 96O
Leu 124
3.4
690
Ile
840
Asp 123
3.3
46O
110
ASD 122
4.0
680
Ile
Pro 121
3.7
32O
2480
Lys 120
3.5
530
970
108
Met 115
3.8
500
400
Ser 109
3.3
52O
340
106
Glu 107
3.6
130
510
Ser 105
3.1
490
3590
Leu 104
3.1
700
1730
Ser 103
3.7
070
326'
102
Gly
48O
125
RESEARCH COMMUNICATIONS
dihedral angle
Ca-Ca bend dist. angle 1
2100
Leu 101
3.3
430
AND BIOPHYSICAL
dihedral angle
Co.-Ca bend dist. angle 1
3130
Glu 76
BIOCHEMICAL
3.1
570
3.1
530
3.5
430
3.4
El0
3.0
410
3.6
930
126
Gly
127
Gly
128
Asn 129
3.5
550
Arg
Glu
130
Glu
131
Ser 132
3.3
710
Thr
3.4
450
Lys 134
3.5
810
3.6
580
3.1
860
3.3
430
3.7
56O
3.5
330
3.7
530
Gly
136
Ala
138
Gly
139
Ser
140
Arg
141
Ala
3.9
730
135
Leu 142
3.7
36O
Thr
Asn 137
3.0
290
3.0
440
3.5
470
3.5
740
3.3
810
3.5
600
143
cys 144
3.4
36'
133
Gly
145
Val
146
Ile
147
Gly
148
Ile
149
Ala
150
Lys 151
and Ca-Ca distances ('2) such from
as the
Steinman, Figures
the
Cu,Zn
needed
one shown Naik,
1-3
for in
Fig.
Abernethy,
illustrate
superoxide
constructing
dismutase
the
4.
a wire
The amino
and Hill
(3).
cc-carbon
backbone
subunit 989
from
the
Cc%-Cn bend dist. angle II
1230
590
247O
64O
1370
820
231°
32O
1220
920
1950
85O
3450
790
3270
36O
223O
62O
1340
900
26E"
750
930
400
1190
440
I0
420
1520
510
1980
550
2E"
23O
196"
150
710
570
302O
490
1340
180
32'
540
2420 (62O)
26'
3.3 3.6
2.8 3.3 3.7 3.1 3.0 3.5 3.3 2.8 3.3 3.6 3.2 3.4 3.4 3.3 3.1 3.3 3.5 4.0 3.7
(710)
backbone
acid
4.0
3.0
76O
3180
3.3
3.6
810
2590
3.3
model
sequence
conformation averaged
coordi-
is
of
Vol. 63, No. 4, 1975
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
Fig. 1 - Stereo drawing of the e-carbon backbone of the Cu,Zn superoxide dismutase subunit, viewed down the +z coordinate axis. Both here and in Fig. 2 the disulfide bridge is indicated by a thin line, and the a-carbons of the 7 residues which contribute ligands to the metals are shown as solid circles.
Fig. 2 - Stereo drawing of the a-carbon backbone of the Cu,Zn superoxide dismutase subunit. The direction of view is about 20° away from the +y coordinate axis (the local twofold axis of the dimer) and approximately down the axis of the f3 barrel.
nates.
They are
ORTEP program.
redrawn
from
The dominant
plots structural
990
produced feature
by Carroll
Johnson's
of
molecule
this
Vol. 63, No. 4, 1975
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
Ll”ll of antiparallel $ structure in Cu,Zn supFig. 3 - The 8 strands The line eroxide dismutase, viewed from on end of the 6 barrel. included are at the lower right is a scale in 1 . The residues 25-35,38-46,80-88,91-100,113-118, and 142-150. 2-11, 13-24,
of a wire backbone model of the Cu,Zn superFig. 4 - Photograph oxide dismutase produced from the bend angles and distances listed in Table II. The disulfide bridge (at upper left) is indicated by a thin wire. The direction of view is approximately down the -x coordinate axis, perpendicular to the views in Fig. 1 and 2.
991
Vol. 63, No. 4,1975
is
BIOCHEMICAL
an E-stranded
viewed ture
from
of
one end in
Fig.
and the
where
the
spacing
slight
barrel
strands
most
front
produced
which
at
2,
and zinc
and they 8 barrel. His 81.
only
bound
the
There
zinc
is
interaction in
down the
105-113,
the
exposed
ligands
the
reference
left
twofold of
and 145-151
the
the
the
2
patterns the
the
8 sheet,
back
set
of
projection. is
directly
below
loops.
loops
the
The cop-
a common histidine
ligand,
and one side
of
the
from
His
44,
His
46,
His
61,
His
61,
His
69,
His
78,
and Asp
from
bridge
between
2 subunits
of
(1).
In Fig.
axis,
the
at the
that
that
cross
external
external
with
contact
and
Cys 55 and Cys 144.
a dimer
is
discussed
2, which
is
viewed
second
one shown,
but
of
that
1,
and uniform
twist to
a-helix
with
are
are
a disulfide
local the
of
ligands
between
lustrated
section
the
Fig.
Diamond-shaped
45O in
two
close
bonding),
4 8 strands
about
between
quite
apart.
6x apart,
The copper
118;
and to
of
In
is curva-
can be seen
characteristic
of
smooth
bottom.
it
is
which
fairly
to
one side,
far
set
on one of
top
hydrogen
4 by the
short
the
8 strands
rather
an angle
are
are
the
front
The one very Fig.
from from
RESEARCH COMMUNICATIONS
B structure,
3, showing
extensive
Fig.
the
4 8 strands
per
of
are
in
causes
Zn in
shown
indicating in
antiparallel
flattening is
between
(probably
are
barrel
AND BIOPHYSICAL
subunit residues
would 1,
The and
il-
almost lie
5-7,
above 17,
47-52,
surface.
ACKNOWLEDGEMENTS This Institutes
work was supported of Health.
by grant
GM 15000
from
the
National
REFERENCES 1.
Richardson, J. S., Thomas, K. A. Rubin, B. D. C. (1975) Proc. Nat. Acad. SC:. USA, in 2. Rubin, B. H., and Richardson, J. S. (1972) 2381-2385. 3. Steinman, H. M., Naik, V. R., Abernethy, J. (1974) J. Biol. Chem. 249, 7326-7338.
992
H., and Richardson, press. Biopolymers 11, L.,
and Hill,
R. L.
Vol. 63, No. 4,197s
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
ALPHA-CARBON COORDINATES FOR BOVINE CU,ZN SUPEROXIDE DISMUTASE Jane S. Richardson?, Kenneth A. Thomas*, and David C. Richardson* * Department of Biochemistry and +Department of Anatomy, Duke University, Durham, North Carolina 27710. Received
February
26,1975
Summary Preliminary a-carbon and metal coordinates are given for a subunit of the bovine erythrocyte Cutt,Zntt superoxide dismutase. The coordinates are avera ed from 5 sets of measurements made on electron density maps at 3 fi resolution: one set from an averaged map and one set from each of the 4 crystallographically independent subunits (2 dimeric molecules) in the asymmetric unit of the crystal. The 3-dimensional structure of the polypeptide backbone is illustrated and briefly described. The methods graphic
investigation
3x resolution the
listed
here
for
the
or approximate
Bovine C2, with
Cu,Zn
4 subunits
resolution
the
and
map for
zinc each
transforming, the
from
4 subunits.
averaged
map.
a common Cartesian
coordinate
of the
the
Copyright All righrs
dimer
along
per
o I9 75 by Academic Press. Inc. of reproduction in any form reserved.
y axis.
work
of
will
libe con-
coordinates
to
from
are models,
of
5 coordinate with
The 5 sets
space At
group 31
be identical
for
e-carbon,
cop-
the
An averaged
986
unit.
subunits.
measured
system
in
asymmetric appears
and a set All
to
metal
to make backbone
and averaging
calculation,
and the
crystallizes
independent
interpolating,
Fourier the
the
dismutase The course
a-carbon
dismutase
were
crystallo-
calculations.
conformation
coordinates of
traced
wishing
(2 molecules)
backbone
(1).
crystallographic
distance
4 crystallographically
per,
has been
anyone
superoxide
x-ray
superoxide
preliminary
use of
the
elsewhere
the
resolution,
of
Cutt,Zntt
chain
Although
to higher
results
described
backbone
tinued
of
been
identifisd.
drawings,
general
of bovine
have
polypeptide
gands
all
and the
electron
density
map was calculated the
numerical
coordinates sets
were
the
local
were
by
output
was measured transformed twofold
averaged,and
to axis dis-
Vol. 63, No. 4,1975
X
Ala Thr Lys Ala Val Cysh Val Leu Lys Gly Asp Gly Pro Val Gln Gly Thr Ile His Phe Glu Ala Lvs Giy Asp Thr Val Val Val Thr Gly Ser Ile Ti-ir Gly Leu Thr Glu Gly Asp His Gly Phe His Val His Glu Phe Gly Asp
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
cu
8.1 9.1 8.9 6.8 5.7 3.3 2.5 0.5 -0.9 -3.7 -6.3 -5.0 -2.6 -1.2 1.7 ?: 5.2 7.0 6.1 8.0 8.1 9.2 7.6 4.2 4.3 3.8 5.6 5.0 6.7 6.6 5.9 3.3 2.9 0.1 -2.1 -4.7 -4.2 -4.2 -5.6 -6.1 -6.7 -5.8 -6.9 -6.5 -8.9 -9.9 -8.8 -6.8 -8.0 --10.4
BIOCHEMICAL
Y -13.8 -12.7 -8.6 -5.5 -2.2 0.0
z 4.1 6.7 6.7 7.0 5.7 6.8 6.2
8.4 11.2 13.8 15.4 15.3 12.1 9.8 6.8 4.2 0.6 -2.3 -5.8 -9.3 -12.8 -14.6 -17.6 -18.1 -15.1 -11.8 -8.9 -5.4 -2.5 1.0 4.4 6.8 10.8 13.4 12.8 13.0 12.0 9.0 6.4 4.8 2.5 -0.2 -2.2 -3.9 -3.9 -6.1 -4.4 -2.5 0.1
2; Z:i 8.3 11.0 11.2 10.6 10.3 10.5 10.6 11.4 11.0 11.8 11.5 14.0 14.3 15.5 16.9 15.1 16.3 16.1 15.9 15.7 15.6 15.5 15.4 15.1 18.0 20.2 23.8 23.9 23.1 20.0 17.8 16.1 14.5 11.1 7.9 4.9 2.3 0.9 -1.3
-0.6
13.2
AND BIOPHYSICAL
X
Asn Thr Gin Gly cys Thr Ser Ala G1y Pro His Phe Asn Pro Leu Ser Lys Lys His Glv Gl; Pro Lys Asp Glu Glu Arg His Val Gly Asp Leu Gly Asn Val Thr Ala Asp Lys Asn Gly Val Ala Ile Val Aso 11; Val Asp Pro
51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Zn
-7.1 -9.6 -12.2 -10.1 -9.4 -12.7 -12.4 -11.1 -13.1 -13.8 -12.4 -10.6 -12.1 -12.1 -13.8 -16.5 -16.2 -16.7 -14.8 -12.6 -9.5 -6.1 -6.2 -9.5 -11.3 -13.1 -10.9 -10.9 -8.0 -7.6 -7.6 -5.4 -5.4 -4.7 -2.3 -1.1 -0.3 2.0 1.7 3.4 2.4 3.4 3.3 4.8 4.5 4.4 2.9 3.1 0.5 -0.5
RESEARCH COMMUNICATIONS
z Y 3.5 -1.5 4.8 -3.2 6.0 -1.4 7.0 1.0 5.3 3.9 4.8 3.4 2.1 1.7 0.0 3.5 -1.9 5.2 -3.8 7.5 -5.6 10.1 -9.0 9.8 -11.2 10.7 -13.9 9.7 -16.6.10.9 -14.9 12.0 -13.3 14.9 -10.6 17.3 -8.0 18.8 -8.1 20.7 -7.6 22.1 -8.4 21.7 -11.3 23.4 -12.8 23.8 -15.6 22.5 -13.5 20.9 -12.1 19.0 -10.8 15.9 -11.0 13.5 -8.0 13.4 -6.8 16.3 -5.6 17.8 -2.6 20.0 0.3 21.6 2.5 21.2 5.0 23.6 8.6 23.2 12.4 23.9 15.9 24.3 16.7 22.0 13.8 19.8 10.6 19.7 6.6 19.8 3.4 20.4 0.2 18.9 -2.8 20.8 -6.0 19.9 -9.9 20.0 -11.4 18.4 -14.5 18.0
-12.2
-5.7
Leu Ile Ser Leu Se?? Gly Glu Tyr Ser Ile Ile Gly Arg Thr Met Val Val His Glu Lys Pro Asp Asp Leu Gly Arg Gly Gly Asn Glu Glu Ser Thr Lys Thr Gly Asn Ala Gly Ser Arg Leu Ala cys Giy Val Ile Gly Ile Ala Lys
15.4
101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151
x -2.0 -1.2 0.0 1.9 1.6 -1.0 -4.4 -3.6 -2.2 -2.0 -0.9 -2.7 -4.1 -4.9 -3.7 -5.6 -5.6 -8.6 -9.8 -10.8 -10.3 -11.1 -13.2 -12.0 -15.1 -17.5 -19.2 -23.3 -23.6 -23.9 -20.7 -19.0 -19.4 -18.3 -16.0 -15.2 -16.0 -13.1 -14.0 -12.9 -10.4 -7.2 -4.4 -3.9 -2.2 -1.1 0.8 3.6 6.2 9.9 13.6
Y -14.9 -13.3 -14.7 -13.6 -16.4 -17.6 -17.6 -15.2 -12.6 -9.2 -8.2 -6.2 -5.0 -2.4 -0.9 1.3 4.2 5.6 8.4 6.9 4.6 1.2 -0.8 -3.9 -5.6 -4.9 -2.1 -2.5 -1.7 -2.7 -1.2 -3.3 -5.7 -4.4 -1.8 -0.1 2.7 3.6 5.7 7.1 6.8 8.5 7.2 4.8 2.6 -0.3 -3.3 -4.6 -6.8 -6.5 -7.0
Table I - Averaged a-carbon and metal coordinates for a subunit bovine Cu,Zn superoxide dismutase. Coordinates are orthogonal in 8. The t ransformation to obtain coordinates for the second subunit of a dimer molecule is: x1=-x, y'xy, z'=-z. crepancies
were
maps.
The root
dinate
sets
tween
0.8
reexamined mean square
and the and 0.9x.
on the
individual
errors
between
averaged No attempt
coordinates has been
987
electron the given
individual in
Table
made to refine
z 15.3 12.8 9.8 7.2 5.2 4.3 5.3 7.5 5.9 6.4 3.2 1.4 3.8 5.7 8.7 10.8 13.0 14.9 17.3 20.1 22.0 22.0 24.0 23.7 23.6 25.8 25.6 25.4 22.3 18.9 18.3 19.7 18.2 15.4 16.7 19.2 19.2 17.6 15.2 13.0 11.1 10.5 9.6 7.2 5.4 3.0 4.1 2.8 2.2 3.6 3.5
of and
density coorI are
be-
these
co-
Vol. 63, No. 4,1975
dihedral
bend
angle
angle
Ala
1
Thr
2
Lys
3
Ala
4
Val
5
Cysh
6
Val
7
Leu
8
Lys
9
Gly
10
Asp
11
Gly
12
(1800) 00 7E"
Val
14
Gln
15
Gly
16
Thr
17
Ile
18
His
19
123'= 288"
Glu
21
Ala
22
Gly
24
Asp
25
300 500
400
324O 1190
460 28O
161°
20
1970 185O 1770 284O 1200
85O 360 700 310 23O
3470
140
1300
450
326" 152O 3330 164O 190 164O
Lys 23
700
440
1170
Phe 20
(710)
330
3060
Pro 13
BIOCHEMICAL
910
390 500 46'= 330 61'= 65O 540
730
900
Ca-Ccc dist.
or to
Table carbons,
3.1 4.0 3.8 3.7 3.4 3.6 3.2 3.3 4.0 3.6
oxide
3.6 3.5 3.7 3.4 3.5 3.6
26
Val
21
Val
28
Val
29
Thr
30
Gly
31
Ser
32
Ile
33
Thr
34
Gly
35
Thr
37
Glu
38
Gly
39
Asp
40
His
41
Gly
42
3.5 3.7 4.1 3.5 3.3
His
44
Val
45
His
46
Glu
47
40 2090
3.5 3.6
Gly
49
Asp
50
62O
390
2410
32O
246O 242'= 62'= 237O 2940
90 350 42O 42O 750
1170 324O 247O 2010 266'= 63O 356" 161'= 288"
190 62O 710 330 48'= 200 28O 38" 370
1740 220 269O 298O 163O 298O
510 400 770 26" 590 510
dihedral angle
3.3 3.8 3.6 3.6 3.4 3.5 3.5 3.5 4.0 3.9 3.7 3.4
Asn
51
Thr
52
Gln
53
Gly
54
cys
55
Thr
56
Ser
57
Ala
58
Gly
59
Pro
60
His
61
Phe 62
3.8
Asn 63
2.9
1350
Leu 65
3.5
Ser 66
3.3
Lys
3.2
67
Lys 68
2.8 3.8 4.0 3.8 3.3 3.2
His
69
Gly
70
Gly
71
Pro
72
Lys
73
Glu
64O
262O
880
16S" 126O 217O
550 1040
2790 90 208" 206O 1220 18" 164O 3410 16O 2970 730 3300 261° 220 3190 233O 253O 10
Asp 74
3.6
7E"
226O
Pro 64
3.1
Ca-Ca
bend dist. angle R
251°
75
830 710 6S" 26O 390 56O 65O 52O 52'= 83O 62O 220 410 490 210 350 83O 6LI" 420 930
3.6 3.3 3.4 3.3 3.4 3.4 3.1 3.1 3.2 3.2 3.5 3.8 2.9 2.9 3.3 3.3 3.4 3.6 3.5 3.0 3.4 3.5 3.4 3.7 3.5
angles and a-carbon to cl-carbon distances a wire backbone model (2) of the bovine Cu,Zn Such a model is shown in Fig. 4. subunit.
adjust
them
these
Table
530
470
61°
Phe 48
RESEARCH COMMUNICATIONS
ca-ca bend dist. angle 1
1510
Phe 43
copper,
dismutase;
Thr
Leu 36
3.2
I lists the
dihed??a1 angle
8
Table II - The bend needed to construct superoxide dismutase
ordinates
AND BIOPHYSICAL
to
give
averaged
and the II
lists
standard
Ca-Ccr distances.
coordinates
zinc
of the 988
one subunit bend
angles,
for
the of
151 ccCu,Zn
dihedral
superangles,
Vol. 63, No. 4,1975
dihedFdl angle
Arg
77
His
78
Val
79
Gly
80
Asp
81
990 3150 1980 248O 0* 1360
Leu 82 Gly
10
83
5*
Ash 84 Val
85
Thr
86
Ala
87
Asp
88
Lys
83
2060 120 2910 146O 250 60°
Asn 90 Gly
91
Val
92
Ala
93
Ile
94
Val
95
Asp
96
Ile
97
Val
98
338O 1060 312O 164O 220 1770 322O 142O 32Ei"
Asp 33 Pro
100
1770
3.2
780
Ile
3.3
560
Gly
2.9
480
Tyr
3.5
490
3.7
490
3.1
250
4.5
36O
3.6
83O
3.0
85O
3.4
200
4.1
27O
3.6
46O
3.5
58O
111
Gly
112
Arg
113
Thr
114
203O 226O 34E" 252O 920
Val
116
Val
117
His
118
Glu
119
306O 1280 3100 1920 226O 1470 340 237O 96O
Leu 124
3.4
690
Ile
840
Asp 123
3.3
46O
110
ASD 122
4.0
680
Ile
Pro 121
3.7
32O
2480
Lys 120
3.5
530
970
108
Met 115
3.8
500
400
Ser 109
3.3
52O
340
106
Glu 107
3.6
130
510
Ser 105
3.1
490
3590
Leu 104
3.1
700
1730
Ser 103
3.7
070
326'
102
Gly
48O
125
RESEARCH COMMUNICATIONS
dihedral angle
Ca-Ca bend dist. angle 1
2100
Leu 101
3.3
430
AND BIOPHYSICAL
dihedral angle
Co.-Ca bend dist. angle 1
3130
Glu 76
BIOCHEMICAL
3.1
570
3.1
530
3.5
430
3.4
El0
3.0
410
3.6
930
126
Gly
127
Gly
128
Asn 129
3.5
550
Arg
Glu
130
Glu
131
Ser 132
3.3
710
Thr
3.4
450
Lys 134
3.5
810
3.6
580
3.1
860
3.3
430
3.7
56O
3.5
330
3.7
530
Gly
136
Ala
138
Gly
139
Ser
140
Arg
141
Ala
3.9
730
135
Leu 142
3.7
36O
Thr
Asn 137
3.0
290
3.0
440
3.5
470
3.5
740
3.3
810
3.5
600
143
cys 144
3.4
36'
133
Gly
145
Val
146
Ile
147
Gly
148
Ile
149
Ala
150
Lys 151
and Ca-Ca distances ('2) such from
as the
Steinman, Figures
the
Cu,Zn
needed
one shown Naik,
1-3
for in
Fig.
Abernethy,
illustrate
superoxide
constructing
dismutase
the
4.
a wire
The amino
and Hill
(3).
cc-carbon
backbone
subunit 989
from
the
Cc%-Cn bend dist. angle II
1230
590
247O
64O
1370
820
231°
32O
1220
920
1950
85O
3450
790
3270
36O
223O
62O
1340
900
26E"
750
930
400
1190
440
I0
420
1520
510
1980
550
2E"
23O
196"
150
710
570
302O
490
1340
180
32'
540
2420 (62O)
26'
3.3 3.6
2.8 3.3 3.7 3.1 3.0 3.5 3.3 2.8 3.3 3.6 3.2 3.4 3.4 3.3 3.1 3.3 3.5 4.0 3.7
(710)
backbone
acid
4.0
3.0
76O
3180
3.3
3.6
810
2590
3.3
model
sequence
conformation averaged
coordi-
is
of
Vol. 63, No. 4, 1975
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
Fig. 1 - Stereo drawing of the e-carbon backbone of the Cu,Zn superoxide dismutase subunit, viewed down the +z coordinate axis. Both here and in Fig. 2 the disulfide bridge is indicated by a thin line, and the a-carbons of the 7 residues which contribute ligands to the metals are shown as solid circles.
Fig. 2 - Stereo drawing of the a-carbon backbone of the Cu,Zn superoxide dismutase subunit. The direction of view is about 20° away from the +y coordinate axis (the local twofold axis of the dimer) and approximately down the axis of the f3 barrel.
nates.
They are
ORTEP program.
redrawn
from
The dominant
plots structural
990
produced feature
by Carroll
Johnson's
of
molecule
this
Vol. 63, No. 4, 1975
BIOCHEMICAL
AND BIOPHYSICAL
RESEARCH COMMUNICATIONS
Ll”ll of antiparallel $ structure in Cu,Zn supFig. 3 - The 8 strands The line eroxide dismutase, viewed from on end of the 6 barrel. included are at the lower right is a scale in 1 . The residues 25-35,38-46,80-88,91-100,113-118, and 142-150. 2-11, 13-24,
of a wire backbone model of the Cu,Zn superFig. 4 - Photograph oxide dismutase produced from the bend angles and distances listed in Table II. The disulfide bridge (at upper left) is indicated by a thin wire. The direction of view is approximately down the -x coordinate axis, perpendicular to the views in Fig. 1 and 2.
991
Vol. 63, No. 4,1975
is
BIOCHEMICAL
an E-stranded
viewed ture
from
of
one end in
Fig.
and the
where
the
spacing
slight
barrel
strands
most
front
produced
which
at
2,
and zinc
and they 8 barrel. His 81.
only
bound
the
There
zinc
is
interaction in
down the
105-113,
the
exposed
ligands
the
reference
left
twofold of
and 145-151
the
the
the
2
patterns the
the
8 sheet,
back
set
of
projection. is
directly
below
loops.
loops
the
The cop-
a common histidine
ligand,
and one side
of
the
from
His
44,
His
46,
His
61,
His
61,
His
69,
His
78,
and Asp
from
bridge
between
2 subunits
of
(1).
In Fig.
axis,
the
at the
that
that
cross
external
external
with
contact
and
Cys 55 and Cys 144.
a dimer
is
discussed
2, which
is
viewed
second
one shown,
but
of
that
1,
and uniform
twist to
a-helix
with
are
are
a disulfide
local the
of
ligands
between
lustrated
section
the
Fig.
Diamond-shaped
45O in
two
close
bonding),
4 8 strands
about
between
quite
apart.
6x apart,
The copper
118;
and to
of
In
is curva-
can be seen
characteristic
of
smooth
bottom.
it
is
which
fairly
to
one side,
far
set
on one of
top
hydrogen
4 by the
short
the
8 strands
rather
an angle
are
are
the
front
The one very Fig.
from from
RESEARCH COMMUNICATIONS
B structure,
3, showing
extensive
Fig.
the
4 8 strands
per
of
are
in
causes
Zn in
shown
indicating in
antiparallel
flattening is
between
(probably
are
barrel
AND BIOPHYSICAL
subunit residues
would 1,
The and
il-
almost lie
5-7,
above 17,
47-52,
surface.
ACKNOWLEDGEMENTS This Institutes
work was supported of Health.
by grant
GM 15000
from
the
National
REFERENCES 1.
Richardson, J. S., Thomas, K. A. Rubin, B. D. C. (1975) Proc. Nat. Acad. SC:. USA, in 2. Rubin, B. H., and Richardson, J. S. (1972) 2381-2385. 3. Steinman, H. M., Naik, V. R., Abernethy, J. (1974) J. Biol. Chem. 249, 7326-7338.
992
H., and Richardson, press. Biopolymers 11, L.,
and Hill,
R. L.
