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1G55
Asym. Unit
Info
Asym.Unit (63 KB)
Biol.Unit 1 (58 KB)
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(1)
Title
:
STRUCTURE OF HUMAN DNMT2, AN ENIGMATIC DNA METHYLTRANSFERASE HOMOLOGUE
Authors
:
A. Dong, J. A. Yoder, X. Zhang, L. Zhou, T. H. Bestor, X. Cheng
Date
:
30 Oct 00 (Deposition) - 17 Jan 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Human Dna Methyltransferase Homologue, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Dong, J. A. Yoder, X. Zhang, L. Zhou, T. H. Bestor, X. Cheng
Structure Of Human Dnmt2, An Enigmatic Dna Methyltransferas Homolog That Displays Denaturant-Resistant Binding To Dna.
Nucleic Acids Res. V. 29 439 2001
[
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
2a: S-HYDROXYCYSTEINE (CSOa)
2b: S-HYDROXYCYSTEINE (CSOb)
3a: GLYCEROL (GOLa)
4a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
5a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
1
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CSO
2
Mod. Amino Acid
S-HYDROXYCYSTEINE
3
GOL
1
Ligand/Ion
GLYCEROL
4
SAH
1
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
5
SO4
1
Ligand/Ion
SULFATE ION
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:61 , LEU A:62 , HIS A:101 , ILE A:105 , ARG A:108 , LYS A:334 , HOH A:488
BINDING SITE FOR RESIDUE SO4 A 399
2
AC2
SOFTWARE
TYR A:10 , SER A:11 , GLY A:12 , VAL A:13 , GLY A:15 , ASP A:34 , VAL A:35 , ASN A:36 , LYS A:55 , THR A:56 , ILE A:57 , GLU A:58 , SER A:76 , PRO A:78 , SER A:98 , ASN A:375 , SER A:376 , HOH A:414 , HOH A:427 , HOH A:459 , HOH A:495 , HOH A:657
BINDING SITE FOR RESIDUE SAH A 392
3
AC3
SOFTWARE
HIS A:18 , ARG A:21 , GLU A:22 , CYS A:24 , ASN A:46 , PHE A:47 , GLU A:357 , HOH A:637
BINDING SITE FOR RESIDUE BME A 395
4
AC4
SOFTWARE
LEU A:279 , ASP A:281 , VAL A:291 , ILE A:301 , GLU A:302 , GLY A:303 , THR A:304 , GLY A:305
BINDING SITE FOR RESIDUE GOL A 397
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_051961 (H101Y, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051961
H
101
Y
TRDMT_HUMAN
Polymorphism
11254413
A
H
101
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: SAM_MT_C5 (A:4-391)
2: C5_MTASE_2 (A:371-389)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SAM_MT_C5
PS51679
C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
TRDMT_HUMAN
4-391
1
A:4-391
2
C5_MTASE_2
PS00095
C-5 cytosine-specific DNA methylases C-terminal signature.
TRDMT_HUMAN
371-389
1
A:371-389
[
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Exons
(11, 11)
Info
All Exons
Exon 1.1d (A:2-22)
Exon 1.4b (A:22-58)
Exon 1.9 (A:59-78)
Exon 1.10 (A:97-108)
Exon 1.11 (A:108-130)
Exon 1.12 (A:130-153)
Exon 1.13b (A:154-181)
Exon 1.14b (A:182-296 (gaps))
Exon 1.15 (A:296-315)
Exon 1.16a (A:316-359)
Exon 1.18e (A:359-391)
View:
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All Exon Boundaries
01: Boundary -/1.1d
02: Boundary 1.1d/1.4b
03: Boundary 1.4b/1.9
04: Boundary 1.9/1.10
05: Boundary 1.10/1.11
06: Boundary 1.11/1.12
07: Boundary 1.12/1.13b
08: Boundary 1.13b/1.14b
09: Boundary 1.14b/1.15
10: Boundary 1.15/1.16a
11: Boundary 1.16a/1.18e
12: Boundary 1.18e/-
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
1.1d
ENST00000377799
1d
ENSE00002177384
chr10:
17243681-17243570
112
TRDMT_HUMAN
1-22
22
1
A:2-22
21
1.4b
ENST00000377799
4b
ENSE00001771809
chr10:
17216659-17216550
110
TRDMT_HUMAN
22-58
37
1
A:22-58
37
1.9
ENST00000377799
9
ENSE00000692747
chr10:
17210916-17210840
77
TRDMT_HUMAN
59-84
26
1
A:59-78
20
1.10
ENST00000377799
10
ENSE00001695747
chr10:
17204236-17204165
72
TRDMT_HUMAN
84-108
25
1
A:97-108
12
1.11
ENST00000377799
11
ENSE00001676885
chr10:
17203547-17203482
66
TRDMT_HUMAN
108-130
23
1
A:108-130
23
1.12
ENST00000377799
12
ENSE00001706222
chr10:
17202373-17202304
70
TRDMT_HUMAN
130-153
24
1
A:130-153
24
1.13b
ENST00000377799
13b
ENSE00001756222
chr10:
17201228-17201145
84
TRDMT_HUMAN
154-181
28
1
A:154-181
28
1.14b
ENST00000377799
14b
ENSE00001726563
chr10:
17199783-17199440
344
TRDMT_HUMAN
182-296
115
1
A:182-296 (gaps)
115
1.15
ENST00000377799
15
ENSE00001652345
chr10:
17196733-17196676
58
TRDMT_HUMAN
296-315
20
1
A:296-315
20
1.16a
ENST00000377799
16a
ENSE00001612374
chr10:
17195635-17195506
130
TRDMT_HUMAN
316-359
44
1
A:316-359
44
1.18e
ENST00000377799
18e
ENSE00001935652
chr10:
17191139-17188736
2404
TRDMT_HUMAN
359-391
33
1
A:359-391
33
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1g55a_ (A:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
C5 cytosine-specific DNA methylase, DCM
(32)
Protein domain
:
DNMT2
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1g55a_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1g55A02 (A:2-186,A:378-391)
2a: CATH_1g55A01 (A:187-377)
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Human (Homo sapiens)
(49)
1a
1g55A02
A:2-186,A:378-391
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
DNA Methylase; Chain A, domain 2
(31)
Homologous Superfamily
:
DNA Methylase, subunit A, domain 2
(31)
Human (Homo sapiens)
(1)
2a
1g55A01
A:187-377
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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