Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8G57

Structure of nucleosome-bound Sirtuin 6 deacetylase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
A	0046982	molecular_function	protein heterodimerization activity
B	0003677	molecular_function	DNA binding
B	0030527	molecular_function	structural constituent of chromatin
B	0046982	molecular_function	protein heterodimerization activity
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0006325	biological_process	chromatin organization
C	0008285	biological_process	negative regulation of cell population proliferation
C	0030527	molecular_function	structural constituent of chromatin
C	0031492	molecular_function	nucleosomal DNA binding
C	0031507	biological_process	heterochromatin formation
C	0043505	cellular_component	CENP-A containing nucleosome
C	0046982	molecular_function	protein heterodimerization activity
C	0061644	biological_process	protein localization to CENP-A containing chromatin
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
D	0001530	molecular_function	lipopolysaccharide binding
D	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005615	cellular_component	extracellular space
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005694	cellular_component	chromosome
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0031640	biological_process	killing of cells of another organism
D	0042742	biological_process	defense response to bacterium
D	0043505	cellular_component	CENP-A containing nucleosome
D	0046982	molecular_function	protein heterodimerization activity
D	0050829	biological_process	defense response to Gram-negative bacterium
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061644	biological_process	protein localization to CENP-A containing chromatin
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
E	0046982	molecular_function	protein heterodimerization activity
F	0003677	molecular_function	DNA binding
F	0030527	molecular_function	structural constituent of chromatin
F	0046982	molecular_function	protein heterodimerization activity
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0006325	biological_process	chromatin organization
G	0008285	biological_process	negative regulation of cell population proliferation
G	0030527	molecular_function	structural constituent of chromatin
G	0031492	molecular_function	nucleosomal DNA binding
G	0031507	biological_process	heterochromatin formation
G	0043505	cellular_component	CENP-A containing nucleosome
G	0046982	molecular_function	protein heterodimerization activity
G	0061644	biological_process	protein localization to CENP-A containing chromatin
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
H	0001530	molecular_function	lipopolysaccharide binding
H	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005615	cellular_component	extracellular space
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005694	cellular_component	chromosome
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
H	0006325	biological_process	chromatin organization
H	0006334	biological_process	nucleosome assembly
H	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0031640	biological_process	killing of cells of another organism
H	0042742	biological_process	defense response to bacterium
H	0043505	cellular_component	CENP-A containing nucleosome
H	0046982	molecular_function	protein heterodimerization activity
H	0050829	biological_process	defense response to Gram-negative bacterium
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061644	biological_process	protein localization to CENP-A containing chromatin
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
K	0000122	biological_process	negative regulation of transcription by RNA polymerase II
K	0000781	cellular_component	chromosome, telomeric region
K	0000785	cellular_component	chromatin
K	0003677	molecular_function	DNA binding
K	0003682	molecular_function	chromatin binding
K	0003684	molecular_function	damaged DNA binding
K	0003714	molecular_function	transcription corepressor activity
K	0003723	molecular_function	RNA binding
K	0003950	molecular_function	NAD+-protein poly-ADP-ribosyltransferase activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0005721	cellular_component	pericentric heterochromatin
K	0005730	cellular_component	nucleolus
K	0005783	cellular_component	endoplasmic reticulum
K	0006281	biological_process	DNA repair
K	0006284	biological_process	base-excision repair
K	0006302	biological_process	double-strand break repair
K	0006325	biological_process	chromatin organization
K	0006338	biological_process	chromatin remodeling
K	0006476	biological_process	protein deacetylation
K	0006606	biological_process	protein import into nucleus
K	0008270	molecular_function	zinc ion binding
K	0008285	biological_process	negative regulation of cell population proliferation
K	0008340	biological_process	determination of adult lifespan
K	0009411	biological_process	response to UV
K	0010526	biological_process	retrotransposon silencing
K	0010569	biological_process	regulation of double-strand break repair via homologous recombination
K	0016746	molecular_function	acyltransferase activity
K	0016757	molecular_function	glycosyltransferase activity
K	0016779	molecular_function	nucleotidyltransferase activity
K	0017136	molecular_function	NAD-dependent histone deacetylase activity
K	0019216	biological_process	regulation of lipid metabolic process
K	0031490	molecular_function	chromatin DNA binding
K	0031491	molecular_function	nucleosome binding
K	0031508	biological_process	pericentric heterochromatin formation
K	0031509	biological_process	subtelomeric heterochromatin formation
K	0031648	biological_process	protein destabilization
K	0032024	biological_process	positive regulation of insulin secretion
K	0032129	molecular_function	histone H3K9 deacetylase activity
K	0032206	biological_process	positive regulation of telomere maintenance
K	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
K	0032922	biological_process	circadian regulation of gene expression
K	0034244	biological_process	negative regulation of transcription elongation by RNA polymerase II
K	0034979	molecular_function	NAD-dependent protein lysine deacetylase activity
K	0035861	cellular_component	site of double-strand break
K	0042181	biological_process	ketone biosynthetic process
K	0042308	biological_process	negative regulation of protein import into nucleus
K	0042593	biological_process	glucose homeostasis
K	0042752	biological_process	regulation of circadian rhythm
K	0042803	molecular_function	protein homodimerization activity
K	0043231	cellular_component	intracellular membrane-bounded organelle
K	0043687	biological_process	post-translational protein modification
K	0045600	biological_process	positive regulation of fat cell differentiation
K	0045721	biological_process	negative regulation of gluconeogenesis
K	0045814	biological_process	negative regulation of gene expression, epigenetic
K	0045820	biological_process	negative regulation of glycolytic process
K	0045892	biological_process	negative regulation of DNA-templated transcription
K	0046325	biological_process	negative regulation of D-glucose import
K	0046827	biological_process	positive regulation of protein export from nucleus
K	0046872	molecular_function	metal ion binding
K	0046969	molecular_function	NAD-dependent histone H3K9 deacetylase activity
K	0048146	biological_process	positive regulation of fibroblast proliferation
K	0050708	biological_process	regulation of protein secretion
K	0050994	biological_process	regulation of lipid catabolic process
K	0051697	biological_process	protein delipidation
K	0055007	biological_process	cardiac muscle cell differentiation
K	0070403	molecular_function	NAD+ binding
K	0090734	cellular_component	site of DNA damage
K	0097372	molecular_function	NAD-dependent histone H3K18 deacetylase activity
K	0099115	cellular_component	chromosome, subtelomeric region
K	0106222	molecular_function	lncRNA binding
K	0106274	molecular_function	NAD+-protein-arginine ADP-ribosyltransferase activity
K	0120162	biological_process	positive regulation of cold-induced thermogenesis
K	0120186	biological_process	negative regulation of protein localization to chromatin
K	0120187	biological_process	positive regulation of protein localization to chromatin
K	0140612	molecular_function	DNA damage sensor activity
K	0140765	molecular_function	NAD-dependent histone H3K56 deacetylase activity
K	0140773	molecular_function	NAD-dependent protein demyristoylase activity
K	0140774	molecular_function	NAD-dependent protein depalmitoylase activity
K	0140804	molecular_function	NAD+-protein-lysine ADP-ribosyltransferase activity
K	0140861	biological_process	DNA repair-dependent chromatin remodeling
K	1902459	biological_process	positive regulation of stem cell population maintenance
K	1902732	biological_process	positive regulation of chondrocyte proliferation
K	1903076	biological_process	regulation of protein localization to plasma membrane
K	1904841	molecular_function	TORC2 complex binding
K	1905555	biological_process	positive regulation of blood vessel branching
K	1905564	biological_process	positive regulation of vascular endothelial cell proliferation
K	1990166	biological_process	protein localization to site of double-strand break
K	1990404	molecular_function	NAD+-protein ADP-ribosyltransferase activity
K	2000648	biological_process	positive regulation of stem cell proliferation
K	2000738	biological_process	positive regulation of stem cell differentiation
K	2000773	biological_process	negative regulation of cellular senescence
K	2000781	biological_process	positive regulation of double-strand break repair

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA21-VAL27

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS14-LEU20

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG92-GLY114

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
A	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by HASPIN and VRK1 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR3
E	THR3

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:12138181

Chain	Residue	Details
A	LYS4
E	LYS4
F	LYS31
F	LYS91

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	GLN5
H	LYS8
H	LYS12
H	LYS13
H	LYS17
H	LYS20
H	LYS40
H	LYS82
E	GLN5
D	LYS15
D	LYS16
D	LYS20
D	LYS23
D	LYS43
D	LYS85
H	LYS2

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphothreonine; by PKC => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR6
A	THR11
E	THR6
E	THR11

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250

Chain	Residue	Details
A	ARG8
E	ARG8
F	TYR51
F	TYR88

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000305\|PubMed:12138181

Chain	Residue	Details
A	LYS9
E	LYS9

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER10
E	SER10
G	LYS74
G	LYS75

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
A	LYS14
E	LYS14
D	LYS120
H	LYS31
H	LYS113
H	LYS117

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: Citrulline; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	ARG17
E	ARG17
C	LYS125
G	LYS118
G	LYS119
G	LYS125

site_id	SWS_FT_FI10
Number of Residues	10
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS18
E	LYS64
A	LYS23
A	LYS27
A	LYS36
A	LYS64
E	LYS18
E	LYS23
E	LYS27
E	LYS36

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: Citrulline => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	ARG26
E	ARG26
H	LYS43
H	LYS105

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER28
E	SER28
G	LYS119

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: N6-methyllysine => ECO:0000250\|UniProtKB:P68431

Chain	Residue	Details
A	LYS37
E	LYS37

site_id	SWS_FT_FI14
Number of Residues	2
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	TYR41
E	TYR41
H	ARG83
H	ARG89

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P84228

Chain	Residue	Details
A	LYS56
A	LYS79
E	LYS56
E	LYS79

site_id	SWS_FT_FI16
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	SER57
E	SER57

site_id	SWS_FT_FI17
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR80
A	THR107
E	THR80
E	THR107

site_id	SWS_FT_FI18
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P84243

Chain	Residue	Details
A	SER86
E	SER86
H	LYS117

site_id	SWS_FT_FI19
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS115
E	LYS115

site_id	SWS_FT_FI20
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	LYS122
E	LYS122

site_id	SWS_FT_FI21
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000250\|UniProtKB:Q71DI3

Chain	Residue	Details
A	CYS110
E	CYS110

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)