Structure of PDB 2pvc Chain B

Receptor sequence

>2pvcB (length=347) Species: 9606 (Homo sapiens) [Search protein sequence]

GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDA
LFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGK
VHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVP
VWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVE
EWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPGPFFWM
FVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSR
HWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST

3D structure

PDB

2pvc DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.

Chain

Resolution

3.69 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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)
BS01	peptide	B	D88 D90 Q93 E103 T104 L105 L106 I107 V134 H135 M137	D55 D57 Q60 E70 T71 L72 L73 I74 V101 H102 M104
BS02	ZN	B	C96 C99 C118 C121	C63 C66 C85 C88
BS03	ZN	B	C108 C113 C142 C145	C75 C80 C109 C112
BS04	ZN	B	C53 C56 C73 C76	C20 C23 C40 C43

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0005515	protein binding
GO:0008047	enzyme activator activity
GO:0019899	enzyme binding
GO:0046872	metal ion binding
GO:0051718	DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0001890	placenta development
GO:0006346	DNA methylation-dependent heterochromatin formation
GO:0007141	male meiosis I
GO:0007283	spermatogenesis
GO:0010468	regulation of gene expression
GO:0010558	negative regulation of macromolecule biosynthetic process
GO:0030154	cell differentiation
GO:0032259	methylation
GO:0044726	epigenetic programing of female pronucleus
GO:0045814	negative regulation of gene expression, epigenetic
GO:0048863	stem cell differentiation
GO:0060718	chorionic trophoblast cell differentiation
GO:0071514	genomic imprinting
GO:0090310	negative regulation of DNA methylation-dependent heterochromatin formation
GO:0141005	retrotransposon silencing by heterochromatin formation
GO:0141068	autosome genomic imprinting
GO:0141196	retrotransposon silencing by piRNA-directed DNA methylation

	Cellular Component
GO:0000792	heterochromatin
GO:0000794	condensed nuclear chromosome
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0035098	ESC/E(Z) complex
GO:1902494	catalytic complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:2pvc, PDBe:2pvc, PDBj:2pvc
PDBsum	2pvc
PubMed	17687327
UniProt	Q9UJW3\|DNM3L_HUMAN DNA (cytosine-5)-methyltransferase 3-like (Gene Name=DNMT3L)

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