9LPK

Structure of human PADI6-UHRF1-UBE2D3 complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000724	biological_process	double-strand break repair via homologous recombination
A	0000785	cellular_component	chromatin
A	0000791	cellular_component	euchromatin
A	0000792	cellular_component	heterochromatin
A	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
A	0003676	molecular_function	nucleic acid binding
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005657	cellular_component	replication fork
A	0005694	cellular_component	chromosome
A	0005819	cellular_component	spindle
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006950	biological_process	response to stress
A	0006974	biological_process	DNA damage response
A	0008270	molecular_function	zinc ion binding
A	0008327	molecular_function	methyl-CpG binding
A	0016363	cellular_component	nuclear matrix
A	0016567	biological_process	protein ubiquitination
A	0031507	biological_process	heterochromatin formation
A	0035825	biological_process	homologous recombination
A	0040029	biological_process	epigenetic regulation of gene expression
A	0042393	molecular_function	histone binding
A	0042802	molecular_function	identical protein binding
A	0044027	biological_process	negative regulation of gene expression via chromosomal CpG island methylation
A	0044729	molecular_function	hemi-methylated DNA-binding
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0050678	biological_process	regulation of epithelial cell proliferation
A	0051247	biological_process	positive regulation of protein metabolic process
A	0051865	biological_process	protein autoubiquitination
A	0061630	molecular_function	ubiquitin protein ligase activity
A	0062072	molecular_function	histone H3K9me2/3 reader activity
A	0071168	biological_process	protein localization to chromatin
A	0090307	biological_process	mitotic spindle assembly
A	0140006	molecular_function	histone H3 reader activity
A	0140234	molecular_function	histone H3K23 ubiquitin ligase activity
A	0140248	molecular_function	histone H3K18 ubiquitin ligase activity
A	0140612	molecular_function	DNA damage sensor activity
A	0140851	molecular_function	histone H3K14 ubiquitin ligase activity
A	0141055	molecular_function	histone H3 ubiquitin ligase activity
A	0141119	biological_process	chromosomal DNA methylation maintenance following DNA replication
B	0004668	molecular_function	protein-arginine deiminase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005938	cellular_component	cell cortex
B	0015631	molecular_function	tubulin binding
B	0040016	biological_process	embryonic cleavage
B	0040019	biological_process	positive regulation of embryonic development
B	0042802	molecular_function	identical protein binding
B	0044725	biological_process	epigenetic programming in the zygotic pronuclei
B	0045111	cellular_component	intermediate filament cytoskeleton
B	0051293	biological_process	establishment of spindle localization
B	0060473	cellular_component	cortical granule
B	0140089	biological_process	protein storage
B	0140094	molecular_function	structural constituent of cytoplasmic lattice
B	0140095	cellular_component	cytoplasmic lattice
B	1990917	cellular_component	ooplasm
C	0004668	molecular_function	protein-arginine deiminase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005938	cellular_component	cell cortex
C	0015631	molecular_function	tubulin binding
C	0040016	biological_process	embryonic cleavage
C	0040019	biological_process	positive regulation of embryonic development
C	0042802	molecular_function	identical protein binding
C	0044725	biological_process	epigenetic programming in the zygotic pronuclei
C	0045111	cellular_component	intermediate filament cytoskeleton
C	0051293	biological_process	establishment of spindle localization
C	0060473	cellular_component	cortical granule
C	0140089	biological_process	protein storage
C	0140094	molecular_function	structural constituent of cytoplasmic lattice
C	0140095	cellular_component	cytoplasmic lattice
C	1990917	cellular_component	ooplasm
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000209	biological_process	protein polyubiquitination
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0006513	biological_process	protein monoubiquitination
D	0010008	cellular_component	endosome membrane
D	0016567	biological_process	protein ubiquitination
D	0030514	biological_process	negative regulation of BMP signaling pathway
D	0036211	biological_process	protein modification process
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0051865	biological_process	protein autoubiquitination
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061631	molecular_function	ubiquitin conjugating enzyme activity
D	0070062	cellular_component	extracellular exosome
D	0070936	biological_process	protein K48-linked ubiquitination
D	0070979	biological_process	protein K11-linked ubiquitination
D	0085020	biological_process	protein K6-linked ubiquitination
D	1903749	biological_process	positive regulation of protein localization to mitochondrion
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000209	biological_process	protein polyubiquitination
E	0004842	molecular_function	ubiquitin-protein transferase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0006513	biological_process	protein monoubiquitination
E	0010008	cellular_component	endosome membrane
E	0016567	biological_process	protein ubiquitination
E	0030514	biological_process	negative regulation of BMP signaling pathway
E	0036211	biological_process	protein modification process
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0051865	biological_process	protein autoubiquitination
E	0061630	molecular_function	ubiquitin protein ligase activity
E	0061631	molecular_function	ubiquitin conjugating enzyme activity
E	0070062	cellular_component	extracellular exosome
E	0070936	biological_process	protein K48-linked ubiquitination
E	0070979	biological_process	protein K11-linked ubiquitination
E	0085020	biological_process	protein K6-linked ubiquitination
E	1903749	biological_process	positive regulation of protein localization to mitochondrion
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0000724	biological_process	double-strand break repair via homologous recombination
F	0000785	cellular_component	chromatin
F	0000791	cellular_component	euchromatin
F	0000792	cellular_component	heterochromatin
F	0000987	molecular_function	cis-regulatory region sequence-specific DNA binding
F	0003676	molecular_function	nucleic acid binding
F	0004842	molecular_function	ubiquitin-protein transferase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005657	cellular_component	replication fork
F	0005694	cellular_component	chromosome
F	0005819	cellular_component	spindle
F	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0006950	biological_process	response to stress
F	0006974	biological_process	DNA damage response
F	0008270	molecular_function	zinc ion binding
F	0008327	molecular_function	methyl-CpG binding
F	0016363	cellular_component	nuclear matrix
F	0016567	biological_process	protein ubiquitination
F	0031507	biological_process	heterochromatin formation
F	0035825	biological_process	homologous recombination
F	0040029	biological_process	epigenetic regulation of gene expression
F	0042393	molecular_function	histone binding
F	0042802	molecular_function	identical protein binding
F	0044027	biological_process	negative regulation of gene expression via chromosomal CpG island methylation
F	0044729	molecular_function	hemi-methylated DNA-binding
F	0045944	biological_process	positive regulation of transcription by RNA polymerase II
F	0050678	biological_process	regulation of epithelial cell proliferation
F	0051247	biological_process	positive regulation of protein metabolic process
F	0051865	biological_process	protein autoubiquitination
F	0061630	molecular_function	ubiquitin protein ligase activity
F	0062072	molecular_function	histone H3K9me2/3 reader activity
F	0071168	biological_process	protein localization to chromatin
F	0090307	biological_process	mitotic spindle assembly
F	0140006	molecular_function	histone H3 reader activity
F	0140234	molecular_function	histone H3K23 ubiquitin ligase activity
F	0140248	molecular_function	histone H3K18 ubiquitin ligase activity
F	0140612	molecular_function	DNA damage sensor activity
F	0140851	molecular_function	histone H3K14 ubiquitin ligase activity
F	0141055	molecular_function	histone H3 ubiquitin ligase activity
F	0141119	biological_process	chromosomal DNA methylation maintenance following DNA replication

Functional Information from PROSITE/UniProt

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL

Chain	Residue	Details
E	TYR74-LEU89

---

site_id	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. CqHnVCkdCL

Chain	Residue	Details
A	CYS739-LEU748

---

site_id	PS01359
Number of Residues	62
Details	ZF_PHD_1 Zinc finger PHD-type signature. CkhCkddvnrlcrvcachlcggrqdpdkq....................LmCde..Cdma.FHiyCldpplssvpsede................................WyCpeC

Chain	Residue	Details
A	CYS302-CYS363

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Region: {"description":"Required to promote base flipping","evidences":[{"source":"UniProtKB","id":"Q8VDF2","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	12
Details	Region: {"description":"Required for formation of a 5-methylcytosine-binding pocket","evidences":[{"source":"PubMed","id":"18772889","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18772889","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Site: {"description":"Required to confer preferential recognition of cytosine over thymine","evidences":[{"source":"PubMed","id":"18772889","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"25218447","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"22634725","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	292
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---