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3PT6
Asym. Unit
Info
Asym.Unit (322 KB)
Biol.Unit 1 (161 KB)
Biol.Unit 2 (160 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MOUSE DNMT1(650-1602) IN COMPLEX WITH DNA
Authors
:
J. Song, D. J. Patel
Date
:
02 Dec 10 (Deposition) - 29 Dec 10 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,I,J
Biol. Unit 1: A,C,I (1x)
Biol. Unit 2: B,D,J (1x)
Keywords
:
Maintenance Dna Methylation, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Song, O. Rechkoblit, T. H. Bestor, D. J. Patel
Structure Of Dnmt1-Dna Complex Reveals A Role For Autoinhibition In Maintenance Dna Methylation.
Science V. 331 1036 2011
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
1b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SAH
2
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
2
ZN
8
Ligand/Ion
ZINC ION
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:1479 , CYS A:1481 , CYS A:1487 , HIS A:1504
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
CYS A:656 , CYS A:659 , CYS A:662 , CYS A:694
BINDING SITE FOR RESIDUE ZN A 2
03
AC3
SOFTWARE
HIS A:796 , CYS A:823 , CYS A:897 , CYS A:900
BINDING SITE FOR RESIDUE ZN A 3
04
AC4
SOFTWARE
CYS A:667 , CYS A:670 , CYS A:673 , CYS A:689
BINDING SITE FOR RESIDUE ZN A 4
05
AC5
SOFTWARE
HIS B:796 , CYS B:823 , CYS B:897 , CYS B:900
BINDING SITE FOR RESIDUE ZN B 1
06
AC6
SOFTWARE
CYS B:656 , CYS B:659 , CYS B:662 , CYS B:694
BINDING SITE FOR RESIDUE ZN B 2
07
AC7
SOFTWARE
CYS B:1479 , CYS B:1481 , CYS B:1487 , HIS B:1504
BINDING SITE FOR RESIDUE ZN B 3
08
AC8
SOFTWARE
CYS B:667 , CYS B:670 , CYS B:673 , CYS B:689
BINDING SITE FOR RESIDUE ZN B 4
09
AC9
SOFTWARE
HOH A:5 , HOH A:13 , PHE A:1148 , SER A:1149 , GLY A:1152 , GLY A:1153 , LEU A:1154 , GLU A:1171 , MET A:1172 , TRP A:1173 , GLU A:1192 , ASP A:1193 , GLY A:1226 , ASN A:1580 , ALA A:1581 , VAL A:1582
BINDING SITE FOR RESIDUE SAH A 1603
10
BC1
SOFTWARE
HOH B:5 , PHE B:1148 , SER B:1149 , GLY B:1150 , GLY B:1152 , GLY B:1153 , LEU B:1154 , GLU B:1171 , MET B:1172 , TRP B:1173 , ASP B:1193 , CYS B:1194 , GLY B:1226 , ALA B:1581 , VAL B:1582
BINDING SITE FOR RESIDUE SAH B 1603
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 10)
Info
All PROSITE Patterns/Profiles
1: BAH (A:758-884,B:758-884|A:976-1103,B:9...)
2: SAM_MT_C5 (A:1142-1600,B:1142-1600)
3: C5_MTASE_1 (A:1221-1233,B:1221-1233)
4: C5_MTASE_2 (A:1576-1594,B:1576-1594)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BAH
PS51038
BAH domain profile.
DNMT1_MOUSE
758-884
976-1103
4
A:758-884
B:758-884
A:976-1103
B:976-1103
2
SAM_MT_C5
PS51679
C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
DNMT1_MOUSE
1142-1601
2
A:1142-1600
B:1142-1600
3
C5_MTASE_1
PS00094
C-5 cytosine-specific DNA methylases active site.
DNMT1_MOUSE
1221-1233
2
A:1221-1233
B:1221-1233
4
C5_MTASE_2
PS00095
C-5 cytosine-specific DNA methylases C-terminal signature.
DNMT1_MOUSE
1576-1594
2
A:1576-1594
B:1576-1594
[
close PROSITE info
]
Exons
(18, 36)
Info
All Exons
Exon 1.21 (A:651-660 | B:650-660)
Exon 1.22 (A:661-693 | B:661-693)
Exon 1.23 (A:693-742 | B:693-742)
Exon 1.24 (A:743-781 | B:743-781)
Exon 1.25 (A:781-849 | B:781-849)
Exon 1.26 (A:850-895 (gaps) | B:850-895 (gaps...)
Exon 1.27 (A:895-953 | B:895-953)
Exon 1.28 (A:953-1026 | B:953-1026)
Exon 1.29 (A:1026-1090 | B:1026-1090)
Exon 1.30 (A:1091-1115 | B:1091-1112)
Exon 1.31 (A:1139-1162 | B:1138-1162)
Exon 1.32 (A:1162-1256 | B:1162-1256)
Exon 1.33 (A:1256-1303 | B:1256-1303)
Exon 1.34 (A:1304-1359 | B:1304-1359)
Exon 1.35 (A:1359-1418 | B:1359-1418)
Exon 1.36 (A:1419-1484 | B:1419-1484)
Exon 1.37 (A:1484-1577 | B:1484-1577)
Exon 1.38 (A:1578-1600 | B:1578-1600)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.20/1.21
02: Boundary 1.21/1.22
03: Boundary 1.22/1.23
04: Boundary 1.23/1.24
05: Boundary 1.24/1.25
06: Boundary 1.25/1.26
07: Boundary 1.26/1.27
08: Boundary 1.27/1.28
09: Boundary 1.28/1.29
10: Boundary 1.29/1.30
11: Boundary 1.30/1.31
12: Boundary 1.31/1.32
13: Boundary 1.32/1.33
14: Boundary 1.33/1.34
15: Boundary 1.34/1.35
16: Boundary 1.35/1.36
17: Boundary 1.36/1.37
18: Boundary 1.37/1.38
19: Boundary 1.38/1.39
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSMUST00000004202
1
ENSMUSE00000502170
chr9:
20757317-20757152
166
DNMT1_MOUSE
1-27
27
0
-
-
1.2
ENSMUST00000004202
2
ENSMUSE00000217265
chr9:
20747063-20747027
37
DNMT1_MOUSE
27-39
13
0
-
-
1.3
ENSMUST00000004202
3
ENSMUSE00000217269
chr9:
20746250-20746143
108
DNMT1_MOUSE
40-75
36
0
-
-
1.4
ENSMUST00000004202
4
ENSMUSE00000217268
chr9:
20746027-20745817
211
DNMT1_MOUSE
76-146
71
0
-
-
1.5
ENSMUST00000004202
5
ENSMUSE00000440704
chr9:
20744998-20744920
79
DNMT1_MOUSE
146-172
27
0
-
-
1.6
ENSMUST00000004202
6
ENSMUSE00000217242
chr9:
20742590-20742515
76
DNMT1_MOUSE
172-197
26
0
-
-
1.7
ENSMUST00000004202
7
ENSMUSE00000217270
chr9:
20741637-20741606
32
DNMT1_MOUSE
198-208
11
0
-
-
1.8
ENSMUST00000004202
8
ENSMUSE00000217249
chr9:
20741065-20740987
79
DNMT1_MOUSE
208-234
27
0
-
-
1.9
ENSMUST00000004202
9
ENSMUSE00000217261
chr9:
20739003-20738963
41
DNMT1_MOUSE
235-248
14
0
-
-
1.10
ENSMUST00000004202
10
ENSMUSE00000217246
chr9:
20736643-20736559
85
DNMT1_MOUSE
248-276
29
0
-
-
1.11
ENSMUST00000004202
11
ENSMUSE00000489733
chr9:
20734609-20734569
41
DNMT1_MOUSE
277-290
14
0
-
-
1.12
ENSMUST00000004202
12
ENSMUSE00000638437
chr9:
20733573-20733492
82
DNMT1_MOUSE
290-317
28
0
-
-
1.13
ENSMUST00000004202
13
ENSMUSE00000217275
chr9:
20731615-20731551
65
DNMT1_MOUSE
318-339
22
0
-
-
1.14
ENSMUST00000004202
14
ENSMUSE00000297925
chr9:
20731292-20731250
43
DNMT1_MOUSE
339-353
15
0
-
-
1.15
ENSMUST00000004202
15
ENSMUSE00000297902
chr9:
20731155-20731075
81
DNMT1_MOUSE
354-380
27
0
-
-
1.16
ENSMUST00000004202
16
ENSMUSE00000217247
chr9:
20730998-20730889
110
DNMT1_MOUSE
381-417
37
0
-
-
1.17
ENSMUST00000004202
17
ENSMUSE00000217264
chr9:
20728585-20728467
119
DNMT1_MOUSE
417-457
41
0
-
-
1.18
ENSMUST00000004202
18
ENSMUSE00000297849
chr9:
20728238-20728146
93
DNMT1_MOUSE
457-488
32
0
-
-
1.19
ENSMUST00000004202
19
ENSMUSE00000217254
chr9:
20727361-20727210
152
DNMT1_MOUSE
488-538
51
0
-
-
1.20
ENSMUST00000004202
20
ENSMUSE00000217278
chr9:
20726925-20726738
188
DNMT1_MOUSE
539-601
63
0
-
-
1.21
ENSMUST00000004202
21
ENSMUSE00000217272
chr9:
20726644-20726467
178
DNMT1_MOUSE
601-660
60
2
A:651-660
B:650-660
10
11
1.22
ENSMUST00000004202
22
ENSMUSE00000217271
chr9:
20724650-20724553
98
DNMT1_MOUSE
661-693
33
2
A:661-693
B:661-693
33
33
1.23
ENSMUST00000004202
23
ENSMUSE00000217257
chr9:
20724431-20724284
148
DNMT1_MOUSE
693-742
50
2
A:693-742
B:693-742
50
50
1.24
ENSMUST00000004202
24
ENSMUSE00000217252
chr9:
20722994-20722879
116
DNMT1_MOUSE
743-781
39
2
A:743-781
B:743-781
39
39
1.25
ENSMUST00000004202
25
ENSMUSE00000217258
chr9:
20722764-20722560
205
DNMT1_MOUSE
781-849
69
2
A:781-849
B:781-849
69
69
1.26
ENSMUST00000004202
26
ENSMUSE00000217241
chr9:
20722486-20722350
137
DNMT1_MOUSE
850-895
46
2
A:850-895 (gaps)
B:850-895 (gaps)
46
46
1.27
ENSMUST00000004202
27
ENSMUSE00000217263
chr9:
20721914-20721741
174
DNMT1_MOUSE
895-953
59
2
A:895-953
B:895-953
59
59
1.28
ENSMUST00000004202
28
ENSMUSE00000217280
chr9:
20720384-20720166
219
DNMT1_MOUSE
953-1026
74
2
A:953-1026
B:953-1026
74
74
1.29
ENSMUST00000004202
29
ENSMUSE00000217274
chr9:
20718533-20718341
193
DNMT1_MOUSE
1026-1090
65
2
A:1026-1090
B:1026-1090
65
65
1.30
ENSMUST00000004202
30
ENSMUSE00000217277
chr9:
20717100-20717016
85
DNMT1_MOUSE
1091-1119
29
2
A:1091-1115
B:1091-1112
25
22
1.31
ENSMUST00000004202
31
ENSMUSE00000217279
chr9:
20716752-20716624
129
DNMT1_MOUSE
1119-1162
44
2
A:1139-1162
B:1138-1162
24
25
1.32
ENSMUST00000004202
32
ENSMUSE00000217255
chr9:
20716459-20716177
283
DNMT1_MOUSE
1162-1256
95
2
A:1162-1256
B:1162-1256
95
95
1.33
ENSMUST00000004202
33
ENSMUSE00000217262
chr9:
20716002-20715861
142
DNMT1_MOUSE
1256-1303
48
2
A:1256-1303
B:1256-1303
48
48
1.34
ENSMUST00000004202
34
ENSMUSE00000217251
chr9:
20714750-20714584
167
DNMT1_MOUSE
1304-1359
56
2
A:1304-1359
B:1304-1359
56
56
1.35
ENSMUST00000004202
35
ENSMUSE00000516732
chr9:
20714314-20714137
178
DNMT1_MOUSE
1359-1418
60
2
A:1359-1418
B:1359-1418
60
60
1.36
ENSMUST00000004202
36
ENSMUSE00000517723
chr9:
20713729-20713534
196
DNMT1_MOUSE
1419-1484
66
2
A:1419-1484
B:1419-1484
66
66
1.37
ENSMUST00000004202
37
ENSMUSE00000297455
chr9:
20713196-20712916
281
DNMT1_MOUSE
1484-1577
94
2
A:1484-1577
B:1484-1577
94
94
1.38
ENSMUST00000004202
38
ENSMUSE00000217243
chr9:
20712405-20712315
91
DNMT1_MOUSE
1578-1608
31
2
A:1578-1600
B:1578-1600
23
23
1.39
ENSMUST00000004202
39
ENSMUSE00000538826
chr9:
20712005-20711650
356
DNMT1_MOUSE
1608-1620
13
0
-
-
[
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SCOP Domains
(0, 0)
Info
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_DNA_methylase_3pt6B01 (B:1142-1596)
1b: PFAM_DNA_methylase_3pt6B02 (B:1142-1596)
2a: PFAM_BAH_3pt6B03 (B:935-1103)
2b: PFAM_BAH_3pt6B04 (B:935-1103)
2c: PFAM_BAH_3pt6B05 (B:935-1103)
2d: PFAM_BAH_3pt6B06 (B:935-1103)
3a: PFAM_zf_CXXC_3pt6B07 (B:650-694)
3b: PFAM_zf_CXXC_3pt6B08 (B:650-694)
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Clan
:
NADP_Rossmann
(1239)
Family
:
DNA_methylase
(15)
Mus musculus (Mouse)
(2)
1a
DNA_methylase-3pt6B01
B:1142-1596
1b
DNA_methylase-3pt6B02
B:1142-1596
Clan
:
no clan defined [family: BAH]
(7)
Family
:
BAH
(7)
Mus musculus (Mouse)
(2)
2a
BAH-3pt6B03
B:935-1103
2b
BAH-3pt6B04
B:935-1103
2c
BAH-3pt6B05
B:935-1103
2d
BAH-3pt6B06
B:935-1103
Clan
:
no clan defined [family: zf-CXXC]
(8)
Family
:
zf-CXXC
(8)
Mus musculus (Mouse)
(1)
3a
zf-CXXC-3pt6B07
B:650-694
3b
zf-CXXC-3pt6B08
B:650-694
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