0.011471
0.000000
0.000000
0.000000
0.011471
0.000000
0.000000
0.000000
0.011471
0.00000
0.00000
0.00000
Tormo-Mas, M.A.
Donderis, J.
Garcia-Caballer, M.
Alt, A.
Mir-Sanchis, I.
Marina, A.
Penades, J.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
90.00
87.180
87.180
87.180
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Ni 2
58.693
NICKEL (II) ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
NI
N
237
N
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
Y
247
N
C
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
R
C
N
296
N
O
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
N
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
N
322
N
O
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
N
N
336
S
C
N
337
N
C
N
338
N
O
N
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
N
346
N
O
N
347
N
O
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
C
N
366
N
O
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
US
Mol.Cell
MOCEFL
2168
1097-2765
49
947
10.1016/J.MOLCEL.2012.12.013
23333307
Phage Dutpases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-Like Mechanism.
2013
UK
Nature
NATUAS
0006
0028-0836
465
779
10.1038/NATURE09065
20473284
Moonlighting Bacteriophage Proteins Derepress Staphylococcal Pathogenicity Islands.
2010
10.2210/pdb3zf3/pdb
pdb_00003zf3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
ADSC CCD
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
I04-1
Diamond
0.9795
SYNCHROTRON
DIAMOND BEAMLINE I04-1
22617.611
DUTPASE
3.6.1.23
YES
1
man
polymer
58.693
NICKEL (II) ION
2
syn
non-polymer
18.015
water
26
nat
water
no
no
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMTNTLQVKLLSKNARMPERNHKTDAGYDIFSAETVVLEPQEKAVIK
TDVAVSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGIHGNLGINIKNDHEDDKMQTIFLRNIDNEKIFEKERHLYKLGS
YRIEKGERIAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMTNTLQVKLLSKNARMPERNHKTDAGYDIFSAETVVLEPQEKAVIK
TDVAVSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGIHGNLGINIKNDHEDDKMQTIFLRNIDNEKIFEKERHLYKLGS
YRIEKGERIAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
53369
STAPHYLOCOCCUS PHAGE 80ALPHA
469008
ESCHERICHIA COLI
BL21(DE3)
PET28A
PLASMID
2.41
49.00
MOLECULAR REPLACEMENT WAS DONE USING AS MODEL THE STRUCTURE OF BACTERIOPHAGE 80ALPHA DUTPASE IN PRESENCE OF DUPNHPP.
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Other
Refinement description
Structure summary
Database references
Other
Structure summary
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2013-01-30
1
1
2013-03-20
1
2
2013-04-03
1
3
2013-04-17
1
4
2023-12-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE WITH DUPNHPP).
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE D81A MUTANT WITH DUPNHPP).
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE D81N MUTANT WITH DUPNHPP).
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE).
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE Y81A MUTANT WITH DUPNHPP).
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE Y84F MUTANT WITH DUPNHPP).
PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE 80ALPHA DUTPASE D81A D110C S168C MUTANT WITH DUPNHPP).
PDBE
Y
PDBE
2012-12-10
REL
REL
NI
NICKEL (II) ION
HOH
water
3ZEZ
PDB ENTRY 3ZEZ
PDB
experimental model
NI
1157
2
NI
NI
1157
A
NI
1158
2
NI
NI
1158
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
n
1
-33
A
n
2
-32
A
n
3
-31
A
n
4
-30
A
n
5
-29
A
n
6
-28
A
n
7
-27
A
n
8
-26
A
n
9
-25
A
n
10
-24
A
n
11
-23
A
n
12
-22
A
n
13
-21
A
n
14
-20
A
n
15
-19
A
n
16
-18
A
n
17
-17
A
n
18
-16
A
n
19
-15
A
n
20
-14
A
n
21
-13
A
n
22
-12
A
n
23
-11
A
n
24
-10
A
n
25
-9
A
n
26
-8
A
n
27
-7
A
n
28
-6
A
n
29
-5
A
n
30
-4
A
n
31
-3
A
n
32
-2
A
n
33
-1
A
n
34
0
A
n
35
1
A
THR
2
n
36
THR
2
A
ASN
3
n
37
ASN
3
A
THR
4
n
38
THR
4
A
LEU
5
n
39
LEU
5
A
GLN
6
n
40
GLN
6
A
VAL
7
n
41
VAL
7
A
LYS
8
n
42
LYS
8
A
LEU
9
n
43
LEU
9
A
LEU
10
n
44
LEU
10
A
SER
11
n
45
SER
11
A
LYS
12
n
46
LYS
12
A
ASN
13
n
47
ASN
13
A
ALA
14
n
48
ALA
14
A
ARG
15
n
49
ARG
15
A
MET
16
n
50
MET
16
A
PRO
17
n
51
PRO
17
A
GLU
18
n
52
GLU
18
A
ARG
19
n
53
ARG
19
A
ASN
20
n
54
ASN
20
A
HIS
21
n
55
HIS
21
A
LYS
22
n
56
LYS
22
A
THR
23
n
57
THR
23
A
ASP
24
n
58
ASP
24
A
ALA
25
n
59
ALA
25
A
GLY
26
n
60
GLY
26
A
TYR
27
n
61
TYR
27
A
ASP
28
n
62
ASP
28
A
ILE
29
n
63
ILE
29
A
PHE
30
n
64
PHE
30
A
SER
31
n
65
SER
31
A
ALA
32
n
66
ALA
32
A
GLU
33
n
67
GLU
33
A
THR
34
n
68
THR
34
A
VAL
35
n
69
VAL
35
A
VAL
36
n
70
VAL
36
A
LEU
37
n
71
LEU
37
A
GLU
38
n
72
GLU
38
A
PRO
39
n
73
PRO
39
A
GLN
40
n
74
GLN
40
A
GLU
41
n
75
GLU
41
A
LYS
42
n
76
LYS
42
A
ALA
43
n
77
ALA
43
A
VAL
44
n
78
VAL
44
A
ILE
45
n
79
ILE
45
A
LYS
46
n
80
LYS
46
A
THR
47
n
81
THR
47
A
ASP
48
n
82
ASP
48
A
VAL
49
n
83
VAL
49
A
ALA
50
n
84
ALA
50
A
VAL
51
n
85
VAL
51
A
SER
52
n
86
SER
52
A
ILE
53
n
87
ILE
53
A
PRO
54
n
88
PRO
54
A
GLU
55
n
89
GLU
55
A
GLY
56
n
90
GLY
56
A
TYR
57
n
91
TYR
57
A
VAL
58
n
92
VAL
58
A
GLY
59
n
93
GLY
59
A
LEU
60
n
94
LEU
60
A
LEU
61
n
95
LEU
61
A
THR
62
n
96
THR
62
A
SER
63
n
97
SER
63
A
ARG
64
n
98
ARG
64
A
SER
65
n
99
SER
65
A
GLY
66
n
100
GLY
66
A
VAL
67
n
101
VAL
67
A
SER
68
n
102
SER
68
A
SER
69
n
103
SER
69
A
LYS
70
n
104
LYS
70
A
THR
71
n
105
THR
71
A
HIS
72
n
106
HIS
72
A
LEU
73
n
107
LEU
73
A
VAL
74
n
108
VAL
74
A
ILE
75
n
109
ILE
75
A
GLU
76
n
110
GLU
76
A
THR
77
n
111
THR
77
A
GLY
78
n
112
GLY
78
A
LYS
79
n
113
LYS
79
A
ILE
80
n
114
ILE
80
A
ASP
81
n
115
ASP
81
A
ALA
82
n
116
ALA
82
A
GLY
83
n
117
GLY
83
A
ILE
84
n
118
ILE
84
A
HIS
85
n
119
HIS
85
A
GLY
86
n
120
GLY
86
A
ASN
87
n
121
ASN
87
A
LEU
88
n
122
LEU
88
A
GLY
89
n
123
GLY
89
A
ILE
90
n
124
ILE
90
A
ASN
91
n
125
ASN
91
A
ILE
92
n
126
ILE
92
A
LYS
93
n
127
LYS
93
A
ASN
94
n
128
ASN
94
A
ASP
95
n
129
ASP
95
A
HIS
96
n
130
HIS
96
A
GLU
97
n
131
GLU
97
A
ASP
98
n
132
ASP
98
A
ASP
99
n
133
ASP
99
A
LYS
100
n
134
LYS
100
A
MET
101
n
135
MET
101
A
GLN
102
n
136
GLN
102
A
THR
103
n
137
THR
103
A
ILE
104
n
138
ILE
104
A
PHE
105
n
139
PHE
105
A
LEU
106
n
140
LEU
106
A
ARG
107
n
141
ARG
107
A
ASN
108
n
142
ASN
108
A
ILE
109
n
143
ILE
109
A
ASP
110
n
144
ASP
110
A
ASN
111
n
145
ASN
111
A
GLU
112
n
146
GLU
112
A
LYS
113
n
147
LYS
113
A
ILE
114
n
148
ILE
114
A
PHE
115
n
149
PHE
115
A
GLU
116
n
150
GLU
116
A
LYS
117
n
151
LYS
117
A
GLU
118
n
152
GLU
118
A
ARG
119
n
153
ARG
119
A
HIS
120
n
154
HIS
120
A
LEU
121
n
155
LEU
121
A
TYR
122
n
156
TYR
122
A
LYS
123
n
157
LYS
123
A
LEU
124
n
158
LEU
124
A
GLY
125
n
159
GLY
125
A
SER
126
n
160
SER
126
A
TYR
127
n
161
TYR
127
A
ARG
128
n
162
ARG
128
A
ILE
129
n
163
ILE
129
A
GLU
130
n
164
GLU
130
A
LYS
131
n
165
LYS
131
A
GLY
132
n
166
GLY
132
A
GLU
133
n
167
GLU
133
A
ARG
134
n
168
ARG
134
A
ILE
135
n
169
ILE
135
A
ALA
136
n
170
ALA
136
A
GLN
137
n
171
GLN
137
A
LEU
138
n
172
LEU
138
A
VAL
139
n
173
VAL
139
A
ILE
140
n
174
ILE
140
A
VAL
141
n
175
VAL
141
A
PRO
142
n
176
PRO
142
A
ILE
143
n
177
ILE
143
A
TRP
144
n
178
TRP
144
A
THR
145
n
179
THR
145
A
PRO
146
n
180
PRO
146
A
GLU
147
n
181
GLU
147
A
LEU
148
n
182
LEU
148
A
LYS
149
n
183
LYS
149
A
GLN
150
n
184
GLN
150
A
VAL
151
n
185
VAL
151
A
GLU
152
n
186
GLU
152
A
GLU
153
n
187
GLU
153
A
PHE
154
n
188
PHE
154
A
GLU
155
n
189
GLU
155
A
SER
156
n
190
SER
156
A
n
191
157
A
n
192
158
A
n
193
159
A
n
194
160
A
n
195
161
A
n
196
162
A
n
197
163
A
n
198
164
A
n
199
165
A
n
200
166
A
n
201
167
A
n
202
168
A
n
203
169
A
n
204
170
A
author_and_software_defined_assembly
PISA
3
trimeric
9570
-50.6
22470
A
ASP
95
A
OD1
ASP
129
8_544
A
NI
1157
B
NI
NI
1_555
A
ASP
95
A
OD1
ASP
129
11_545
103.4
A
ASP
95
A
OD1
ASP
129
8_544
A
NI
1157
B
NI
NI
1_555
A
ASP
95
A
OD1
ASP
129
1_555
103.5
A
ASP
95
A
OD1
ASP
129
11_545
A
NI
1157
B
NI
NI
1_555
A
ASP
95
A
OD1
ASP
129
1_555
103.5
A
ASP
95
A
OD1
ASP
129
8_544
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
1_555
175.1
A
ASP
95
A
OD1
ASP
129
11_545
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
1_555
78.5
A
ASP
95
A
OD1
ASP
129
1_555
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
1_555
80.3
A
ASP
95
A
OD1
ASP
129
8_544
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
8_544
80.2
A
ASP
95
A
OD1
ASP
129
11_545
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
8_544
175.1
A
ASP
95
A
OD1
ASP
129
1_555
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
8_544
78.6
A
HOH
2009
D
O
HOH
1_555
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
8_544
97.6
A
ASP
95
A
OD1
ASP
129
8_544
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
11_545
78.5
A
ASP
95
A
OD1
ASP
129
11_545
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
11_545
80.2
A
ASP
95
A
OD1
ASP
129
1_555
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
11_545
175.2
A
HOH
2009
D
O
HOH
1_555
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
11_545
97.5
A
HOH
2009
D
O
HOH
8_544
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
11_545
97.5
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
-1.0000000000
0.0000000000
0.0000000000
11_545
y+1/2,-z-1/2,-x
crystal symmetry operation
43.5900000000
-43.5900000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
8_544
-z,x-1/2,-y-1/2
crystal symmetry operation
0.0000000000
-43.5900000000
-43.5900000000
A
N
LYS
8
A
N
LYS
42
A
O
ALA
50
A
O
ALA
84
A
O
ILE
29
A
O
ILE
63
A
N
ILE
135
A
N
ILE
169
A
N
VAL
141
A
N
VAL
175
A
O
VAL
58
A
O
VAL
92
A
N
LEU
61
A
N
LEU
95
A
O
GLY
78
A
O
GLY
112
A
N
LEU
37
A
N
LEU
71
A
O
TYR
127
A
O
TYR
161
A
N
ILE
45
A
N
ILE
79
A
O
ILE
90
A
O
ILE
124
A
N
LYS
93
A
N
LYS
127
A
O
VAL
74
A
O
VAL
108
A
N
THR
103
A
N
THR
137
A
O
TYR
122
A
O
TYR
156
A
O
LEU
106
A
O
LEU
140
A
N
ILE
114
A
N
ILE
148
1
A
NI
1157
B
NI
1
A
CG
LYS
22
A
CG
LYS
56
1
Y
1
A
CD
LYS
22
A
CD
LYS
56
1
Y
1
A
CE
LYS
22
A
CE
LYS
56
1
Y
1
A
NZ
LYS
22
A
NZ
LYS
56
1
Y
1
A
MET
-33
A
MET
1
1
Y
1
A
GLY
-32
A
GLY
2
1
Y
1
A
SER
-31
A
SER
3
1
Y
1
A
SER
-30
A
SER
4
1
Y
1
A
HIS
-29
A
HIS
5
1
Y
1
A
HIS
-28
A
HIS
6
1
Y
1
A
HIS
-27
A
HIS
7
1
Y
1
A
HIS
-26
A
HIS
8
1
Y
1
A
HIS
-25
A
HIS
9
1
Y
1
A
HIS
-24
A
HIS
10
1
Y
1
A
SER
-23
A
SER
11
1
Y
1
A
SER
-22
A
SER
12
1
Y
1
A
GLY
-21
A
GLY
13
1
Y
1
A
LEU
-20
A
LEU
14
1
Y
1
A
VAL
-19
A
VAL
15
1
Y
1
A
PRO
-18
A
PRO
16
1
Y
1
A
ARG
-17
A
ARG
17
1
Y
1
A
GLY
-16
A
GLY
18
1
Y
1
A
SER
-15
A
SER
19
1
Y
1
A
HIS
-14
A
HIS
20
1
Y
1
A
MET
-13
A
MET
21
1
Y
1
A
ALA
-12
A
ALA
22
1
Y
1
A
SER
-11
A
SER
23
1
Y
1
A
MET
-10
A
MET
24
1
Y
1
A
THR
-9
A
THR
25
1
Y
1
A
GLY
-8
A
GLY
26
1
Y
1
A
GLY
-7
A
GLY
27
1
Y
1
A
GLN
-6
A
GLN
28
1
Y
1
A
GLN
-5
A
GLN
29
1
Y
1
A
MET
-4
A
MET
30
1
Y
1
A
GLY
-3
A
GLY
31
1
Y
1
A
ARG
-2
A
ARG
32
1
Y
1
A
GLY
-1
A
GLY
33
1
Y
1
A
SER
0
A
SER
34
1
Y
1
A
MET
1
A
MET
35
1
Y
1
A
VAL
157
A
VAL
191
1
Y
1
A
SER
158
A
SER
192
1
Y
1
A
GLU
159
A
GLU
193
1
Y
1
A
ARG
160
A
ARG
194
1
Y
1
A
GLY
161
A
GLY
195
1
Y
1
A
GLU
162
A
GLU
196
1
Y
1
A
LYS
163
A
LYS
197
1
Y
1
A
GLY
164
A
GLY
198
1
Y
1
A
PHE
165
A
PHE
199
1
Y
1
A
GLY
166
A
GLY
200
1
Y
1
A
SER
167
A
SER
201
1
Y
1
A
SER
168
A
SER
202
1
Y
1
A
GLY
169
A
GLY
203
1
Y
1
A
VAL
170
A
VAL
204
1
Y
1
A
SER
52
-118.83
73.46
127.836
49.40
-64.26
0.918
0.876
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL MET IS NOT TRACED. RESIDUES V157-V170 ARE DISORDERED.
0.27781
0.23242
0.23822
3.10
61.65
517
3661
12.4
99.79
19.460
0.349
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.109
0.80
0.80
1.20
PDB ENTRY 3ZEZ
MAXIMUM LIKELIHOOD
MASK
3.10
61.65
26
1258
2
0
1230
0.004
0.019
1249
0.783
1.966
1686
3.798
5.000
154
29.082
25.172
58
12.873
15.000
238
10.622
15.000
7
0.050
0.200
195
0.004
0.021
919
1.898
12.741
619
3.280
19.104
772
1.588
12.973
630
0.306
0.308
3.184
28
273
20
100.00
3.10
61.70
3ZF3
4199
2.0
0.08
1
6.80
5.0
99.9
0.30
3.10
3.27
2.60
1
5.2
100.0
refinement
REFMAC
5.7.0032
Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y84I mutant).
1
N
N
2
N
N
2
N
N
3
N
N
A
ARG
64
A
ARG
98
HELX_P
A
THR
71
A
THR
105
1
1
8
metalc
2.637
A
ASP
95
A
OD1
ASP
129
8_544
A
NI
1157
B
NI
NI
1_555
metalc
2.637
A
ASP
95
A
OD1
ASP
129
11_545
A
NI
1157
B
NI
NI
1_555
metalc
2.635
A
ASP
95
A
OD1
ASP
129
1_555
A
NI
1157
B
NI
NI
1_555
metalc
1.953
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
1_555
metalc
1.953
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
8_544
metalc
1.955
A
NI
1157
B
NI
NI
1_555
A
HOH
2009
D
O
HOH
11_545
HYDROLASE
HYDROLASE, PATHOGENICITY ISLAND, SAPI INDUCTION, GENE TRANSFER, MOONLIGHTING PROTEINS, DUTPASE, DUTP, G-PROTEIN, P-LOOP
A4ZF98_9CAUD
UNP
1
A4ZF98
1
170
3ZF3
1
170
A4ZF98
A
1
35
204
1
expression tag
MET
-33
3ZF3
A
A4ZF98
UNP
1
1
expression tag
GLY
-32
3ZF3
A
A4ZF98
UNP
2
1
expression tag
SER
-31
3ZF3
A
A4ZF98
UNP
3
1
expression tag
SER
-30
3ZF3
A
A4ZF98
UNP
4
1
expression tag
HIS
-29
3ZF3
A
A4ZF98
UNP
5
1
expression tag
HIS
-28
3ZF3
A
A4ZF98
UNP
6
1
expression tag
HIS
-27
3ZF3
A
A4ZF98
UNP
7
1
expression tag
HIS
-26
3ZF3
A
A4ZF98
UNP
8
1
expression tag
HIS
-25
3ZF3
A
A4ZF98
UNP
9
1
expression tag
HIS
-24
3ZF3
A
A4ZF98
UNP
10
1
expression tag
SER
-23
3ZF3
A
A4ZF98
UNP
11
1
expression tag
SER
-22
3ZF3
A
A4ZF98
UNP
12
1
expression tag
GLY
-21
3ZF3
A
A4ZF98
UNP
13
1
expression tag
LEU
-20
3ZF3
A
A4ZF98
UNP
14
1
expression tag
VAL
-19
3ZF3
A
A4ZF98
UNP
15
1
expression tag
PRO
-18
3ZF3
A
A4ZF98
UNP
16
1
expression tag
ARG
-17
3ZF3
A
A4ZF98
UNP
17
1
expression tag
GLY
-16
3ZF3
A
A4ZF98
UNP
18
1
expression tag
SER
-15
3ZF3
A
A4ZF98
UNP
19
1
expression tag
HIS
-14
3ZF3
A
A4ZF98
UNP
20
1
expression tag
MET
-13
3ZF3
A
A4ZF98
UNP
21
1
expression tag
ALA
-12
3ZF3
A
A4ZF98
UNP
22
1
expression tag
SER
-11
3ZF3
A
A4ZF98
UNP
23
1
expression tag
MET
-10
3ZF3
A
A4ZF98
UNP
24
1
expression tag
THR
-9
3ZF3
A
A4ZF98
UNP
25
1
expression tag
GLY
-8
3ZF3
A
A4ZF98
UNP
26
1
expression tag
GLY
-7
3ZF3
A
A4ZF98
UNP
27
1
expression tag
GLN
-6
3ZF3
A
A4ZF98
UNP
28
1
expression tag
GLN
-5
3ZF3
A
A4ZF98
UNP
29
1
expression tag
MET
-4
3ZF3
A
A4ZF98
UNP
30
1
expression tag
GLY
-3
3ZF3
A
A4ZF98
UNP
31
1
expression tag
ARG
-2
3ZF3
A
A4ZF98
UNP
32
1
expression tag
GLY
-1
3ZF3
A
A4ZF98
UNP
33
1
expression tag
SER
0
3ZF3
A
A4ZF98
UNP
34
1
TYR
engineered mutation
ILE
84
3ZF3
A
A4ZF98
UNP
84
118
2
4
2
3
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLN
6
A
GLN
40
A
LEU
9
A
LEU
43
A
VAL
49
A
VAL
83
A
SER
52
A
SER
86
A
TYR
27
A
TYR
61
A
PHE
30
A
PHE
64
A
ARG
134
A
ARG
168
A
PRO
142
A
PRO
176
A
TYR
57
A
TYR
91
A
SER
63
A
SER
97
A
GLY
78
A
GLY
112
A
ILE
80
A
ILE
114
A
VAL
35
A
VAL
69
A
LEU
37
A
LEU
71
A
TYR
127
A
TYR
161
A
ILE
129
A
ILE
163
A
LYS
42
A
LYS
76
A
LYS
46
A
LYS
80
A
GLY
89
A
GLY
123
A
ASN
94
A
ASN
128
A
LEU
73
A
LEU
107
A
ILE
75
A
ILE
109
A
GLN
102
A
GLN
136
A
THR
103
A
THR
137
A
TYR
122
A
TYR
156
A
LYS
123
A
LYS
157
A
LEU
106
A
LEU
140
A
ARG
107
A
ARG
141
A
LYS
113
A
LYS
147
A
ILE
114
A
ILE
148
BINDING SITE FOR RESIDUE NI A 1157
A
NI
1157
Software
6
BINDING SITE FOR RESIDUE NI A 1158
A
NI
1158
Software
1
A
ASP
95
A
ASP
129
6
8_544
A
ASP
95
A
ASP
129
6
1_555
A
ASP
95
A
ASP
129
6
11_545
A
HOH
2009
D
HOH
6
8_544
A
HOH
2009
D
HOH
6
11_545
A
HOH
2009
D
HOH
6
1_555
A
THR
77
A
THR
111
1
11_545
198
P 21 3