5YKO | pdb_00005yko

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	JmjC	e5ykoA3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC	ECOD (1.6)
A	zf-C5HC2	e5ykoA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C5HC2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02928	C5HC2 zinc finger (zf-C5HC2)	C5HC2 zinc finger	Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [1]. This domain may have a DNA binding function.	Domain
A	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain
A	PF02375	jmjN domain (JmjN)	jmjN domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Probable lysine-specific demethylase JMJ14	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein demethylase activity histone H3 demethylase activity histone demethylase activity demethylase activity histone H3K4 demethylase activity histone H3K4me/H3K4me2/H3K4me3 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen dioxygenase activity oxidoreductase activity 2-oxoglutarate-dependent dioxygenase activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process post-transcriptional regulation of gene expression negative regulation of gene expression regulation of post-transcriptional gene silencing post-transcriptional gene silencing rhythmic process circadian rhythm cellular response to stimulus biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response defense response to symbiont response to external stimulus cell death response to biotic stimulus symbiont-induced defense-related programmed cell death cellular response to stress defense response to other organism response to stress immune system process plant-type hypersensitive response innate immune response response to external biotic stimulus programmed cell death photoperiodism, flowering response to light stimulus multicellular organismal process regulation of developmental process reproductive process regulation of long-day photoperiodism, flowering negative regulation of long-day photoperiodism, flowering developmental process involved in reproduction negative regulation of post-embryonic development multicellular organism development photoperiodism anatomical structure development reproductive structure development regulation of multicellular organismal process post-embryonic development long-day photoperiodism system development developmental process regulation of multicellular organismal development reproductive system development negative regulation of response to stimulus negative regulation of developmental process vegetative to reproductive phase transition of meristem regulation of post-embryonic development long-day photoperiodism, flowering regulation of response to stimulus response to radiation response to abiotic stimulus negative regulation of multicellular organismal process regulation of photoperiodism, flowering developmental growth growth cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression, epigenetic plant organ development regulation of root development root development root system development regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus regulation of response to external stimulus positive regulation of biological process positive regulation of response to stimulus regulation of systemic acquired resistance positive regulation of response to external stimulus regulation of response to stress systemic acquired resistance positive regulation of systemic acquired resistance positive regulation of defense response monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process monocarboxylic acid metabolic process L-pipecolic acid biosynthetic process defense response to bacterium positive regulation of defense response to bacterium response to bacterium regulation of defense response to bacterium flower development reproductive shoot system development shoot system development regulation of reproductive process negative regulation of flower development regulation of flower development regulation of shoot system development negative regulation of reproductive process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II regulation of growth root meristem growth meristem maintenance meristem growth regulation of developmental growth root morphogenesis tissue development regulation of root meristem growth regulation of meristem growth plant organ morphogenesis anatomical structure morphogenesis meristem development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
B [auth P]	H3(1-10)K4me3 peptide	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex nucleosome chromatin chromosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003347	JmjC domain	Domain
A	IPR003349	JmjN domain	Domain
A	IPR003889	FY-rich, C-terminal	Conserved Site
A	IPR004198	Zinc finger, C5HC2-type	Domain
A	IPR003888	FY-rich, N-terminal	Conserved Site
B [auth P]	IPR009072	Histone-fold	Homologous Superfamily
B [auth P]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth P]	IPR000164	Histone H3/CENP-A	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth P]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.