3DB5

Crystal structure of methyltransferase domain of human PR domain-containing protein 4

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SET domain	8088215	3000162	SCOP2B (2022-06-29)
B	SCOP2 Family	Histone lysine methyltransferases	8088214	4000376	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SET domain	8088215	3000162	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF21549	e3db5A1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF21549	ECOD (1.6)
B	PF21549	e3db5B1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF21549	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
B	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21549	PR domain zinc finger protein 2, PR domain (PRDM2_PR)	PR domain zinc finger protein 2, PR domain	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, w ...	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, which is a distinct SET domain, that is responsible for its catalytic activity (this entry). This domain displays a typical SET fold consisting mainly of short beta-strands and intervening loops including a pseudo-knot at the C terminus [1].	Domain
A, B	PF18445	PR zinc knuckle motif (zf_PR_Knuckle)	PR zinc knuckle motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PR domain zinc finger protein 4	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding histone methyltransferase binding protein binding enzyme binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity cation binding ion binding metal ion binding small molecule binding	developmental process cellular developmental process cell differentiation cellular process cell fate commitment cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process developmental process cellular developmental process cell differentiation cellular process cell fate commitment cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process macromolecule metabolic process methylation regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle nucleoplasm membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041493	PRDM4, zinc knuckle motif	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, B	IPR001214	SET domain	Domain
A, B	IPR044404	PRDM4, PR/SET domain	Domain
A, B	IPR017124	PR-domain zinc finger protein PRDM4	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UKN5	osteosarcoma

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 R01GM133198.