1U2Z | pdb_00001u2z

Crystal structure of histone K79 methyltransferase Dot1p from yeast

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1u2zc_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Catalytic, N-terminal domain of histone methyltransferase Dot1l	Catalytic, N-terminal domain of histone methyltransferase Dot1l	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1u2zb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Catalytic, N-terminal domain of histone methyltransferase Dot1l	Catalytic, N-terminal domain of histone methyltransferase Dot1l	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1u2za_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Catalytic, N-terminal domain of histone methyltransferase Dot1l	Catalytic, N-terminal domain of histone methyltransferase Dot1l	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Histone methyltransferase Dot1l, N-terminal catalytic domain-like	8028306	4000542	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8040685	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8040685	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8040685	3000118	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C		e1u2zC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PCMT, Methyltransf_25	F:	ECOD (20:10:01)
B		e1u2zB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PCMT, Methyltransf_25	F:	ECOD (20:10:01)
A		e1u2zA1	A: Rossmann-like	X: Rossmann-related	H: S-adenosyl-L-methionine-dependent methyltransferases	T: DOT1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.260.170	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		CATH (4.3.0)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	1.10.260.170	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	1.10.260.170	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF08123	Histone methylation protein DOT1 (DOT1)	Histone methylation protein DOT1	The DOT1 domain regulates gene expression by methylating histone H3 [1]. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Histone-lysine N-methyltransferase, H3 lysine-79 specific	DNA binding binding nucleic acid binding protein binding histone binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K79 methyltransferase activity lysine N-methyltransferase activity DNA binding binding nucleic acid binding protein binding histone binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K79 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K79 trimethyltransferase activity	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process regulation of cellular component organization negative regulation of heterochromatin formation positive regulation of biological process negative regulation of biological process negative regulation of chromatin organization positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of macromolecule metabolic process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of biosynthetic process regulation of biological process heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process heterochromatin organization gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of heterochromatin organization regulation of macromolecule biosynthetic process metabolic process negative regulation of gene expression, epigenetic macromolecule metabolic process negative regulation of heterochromatin organization regulation of metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process DNA damage tolerance nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress subtelomeric heterochromatin formation constitutive heterochromatin formation DNA repair regulation of cell cycle phase transition sexual reproduction signaling regulation of reproductive process reproductive process meiotic recombination checkpoint signaling negative regulation of cell cycle cell cycle phase transition meiotic cell cycle process intracellular signal transduction cell communication negative regulation of cell cycle phase transition meiotic nuclear division signal transduction cell cycle regulation of cell cycle negative regulation of meiotic nuclear division cell cycle process regulation of meiotic cell cycle regulation of cell cycle process meiotic cell cycle organelle fission negative regulation of cell cycle process meiotic cell cycle checkpoint signaling regulation of organelle organization cell cycle checkpoint signaling regulation of meiotic nuclear division organelle organization nuclear division negative regulation of nuclear division negative regulation of organelle organization negative regulation of reproductive process regulation of nuclear division negative regulation of meiotic cell cycle methylation nucleotide-excision repair DNA recombination recombinational repair DNA damage checkpoint signaling mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling mitotic intra-S DNA damage checkpoint signaling DNA integrity checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process signal transduction in response to DNA damage regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle G1/S phase transition regulation of mitotic cell cycle phase transition mitotic G1 DNA damage checkpoint signaling regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition global genome nucleotide-excision repair	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, telomeric region chromosomal region membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR030445	Histone H3-K79 methyltransferase	Family
A, B, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C	IPR025789	Histone-lysine N-methyltransferase DOT1 domain	Domain
A, B, C	IPR021162	Histone H3-K79 methyltransferase, fungi	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.