Structure of PDB 3pt6 Chain A

Receptor sequence

>3pt6A (length=914) Species: 10090 (Mus musculus)

MKRRRCGVCEVCQQPECGKCKACKDMVKFGGTGRSKQACLKRRCPNLAVK
EADDDEEADDDVSEMPSPKKLHQGKKKKQNKDRISWLGQPMKIEENRTYY
QKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWF
CAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKVIYKAPSENWAMEG
GKTYFFQLWYNQEYARFESPPKTQPTEDNKHKFCLSCIRLAELRQKEMPK
VLEQIEEVDGRVYCSSITKNGVVYRLGDSVYLPPEAFTFNIKVASPVKRP
KKDPVNETLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIHCGKKKGKVN
EADIKLRLYKFYRPENTHRSYNGSYHTDINMLYWSDEEAVVNFSDVQGRC
TVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKNFEDPPNHARSPGNKG
KGLPKLRTLDVFSGCGGLSEGFHQAGISETLWAIEMWDPAAQAFRLNNPG
TTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVEMLCGGPPCQGFSGMN
RFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLT
LRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHV
FAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEIQNGASN
SEIPYNGEPLSWFQRQLRGSHYQPILRDHICKDMSPLVAARMRHIPLFPG
SDWRDLPNIQVRLGDGVIAHKLQYTFHDVKNGYSSTGALRGVCSCAEGKA
CDPESRQFSTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMG
KQGRVLHPEQHRVVSVRECARSQGFPDSYRFFGNILDRHRQVGNAVPPPL
AKAIGLEIKLCLLS

3D structure

• PDB: 3pt6 Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
• Chain: A
• Resolution: 3.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C1229 E1269 R1313 R1315
• Catalytic site (residue number reindexed from 1): C543 E583 R627 R629
• Enzyme Commision number: 2.1.1.37: DNA (cytosine-5-)-methyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	R653 K686 Q687 A688 N1239 R1241 R1278	R3 K36 Q37 A38 N553 R555 R592
BS02	dna	A	R684 S685 K686 K700 R1237	R34 S35 K36 K50 R551
BS03	SAH	A	F1148 S1149 G1153 E1171 M1172 N1580 A1581 V1582	F462 S463 G467 E485 M486 N894 A895 V896
BS04	ZN	A	C1479 C1481 H1504	C793 C795 H818
BS05	ZN	A	C659 C694	C9 C44
BS06	ZN	A	H796 C823 C897 C900	H146 C173 C234 C237
BS07	ZN	A	C670 C673 C689	C20 C23 C39

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0008168 methyltransferase activity
• GO:0008270 zinc ion binding

External links

• PDB: RCSB:3pt6, PDBe:3pt6, PDBj:3pt6
• PDBsum: 3pt6
• PubMed: 21163962
• UniProt: P13864|DNMT1_MOUSE DNA (cytosine-5)-methyltransferase 1 (Gene Name=Dnmt1)