Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4FIP

Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000124	cellular_component	SAGA complex
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0006508	biological_process	proteolysis
A	0008234	molecular_function	cysteine-type peptidase activity
A	0008270	molecular_function	zinc ion binding
A	0008380	biological_process	RNA splicing
A	0016579	biological_process	protein deubiquitination
A	0046695	cellular_component	SLIK (SAGA-like) complex
A	0046872	molecular_function	metal ion binding
A	0060090	molecular_function	molecular adaptor activity
A	0071819	cellular_component	DUBm complex
B	0000124	cellular_component	SAGA complex
B	0000932	cellular_component	P-body
B	0000973	biological_process	post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
B	0003682	molecular_function	chromatin binding
B	0003713	molecular_function	transcription coactivator activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005643	cellular_component	nuclear pore
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0006325	biological_process	chromatin organization
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0006406	biological_process	mRNA export from nucleus
B	0008047	molecular_function	enzyme activator activity
B	0015031	biological_process	protein transport
B	0016973	biological_process	poly(A)+ mRNA export from nucleus
B	0032880	biological_process	regulation of protein localization
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046695	cellular_component	SLIK (SAGA-like) complex
B	0051028	biological_process	mRNA transport
B	0070390	cellular_component	transcription export complex 2
B	0071028	biological_process	nuclear mRNA surveillance
B	0071819	cellular_component	DUBm complex
E	0000124	cellular_component	SAGA complex
E	0004843	molecular_function	cysteine-type deubiquitinase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0006508	biological_process	proteolysis
E	0008234	molecular_function	cysteine-type peptidase activity
E	0008270	molecular_function	zinc ion binding
E	0008380	biological_process	RNA splicing
E	0016579	biological_process	protein deubiquitination
E	0046695	cellular_component	SLIK (SAGA-like) complex
E	0046872	molecular_function	metal ion binding
E	0060090	molecular_function	molecular adaptor activity
E	0071819	cellular_component	DUBm complex
F	0000124	cellular_component	SAGA complex
F	0000932	cellular_component	P-body
F	0000973	biological_process	post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
F	0003682	molecular_function	chromatin binding
F	0003713	molecular_function	transcription coactivator activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005643	cellular_component	nuclear pore
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0006325	biological_process	chromatin organization
F	0006357	biological_process	regulation of transcription by RNA polymerase II
F	0006368	biological_process	transcription elongation by RNA polymerase II
F	0006406	biological_process	mRNA export from nucleus
F	0008047	molecular_function	enzyme activator activity
F	0015031	biological_process	protein transport
F	0016973	biological_process	poly(A)+ mRNA export from nucleus
F	0032880	biological_process	regulation of protein localization
F	0045893	biological_process	positive regulation of DNA-templated transcription
F	0045944	biological_process	positive regulation of transcription by RNA polymerase II
F	0046695	cellular_component	SLIK (SAGA-like) complex
F	0051028	biological_process	mRNA transport
F	0070390	cellular_component	transcription export complex 2
F	0071028	biological_process	nuclear mRNA surveillance
F	0071819	cellular_component	DUBm complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 501

Chain	Residue
A	CYS4
A	HIS6
A	CYS96
A	CYS99

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 502

Chain	Residue
A	CYS46
A	CYS49
A	CYS68
A	HIS73

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 503

Chain	Residue
A	CYS63
A	HIS77
A	HIS83
A	CYS60

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 504

Chain	Residue
A	HIS250
A	CYS271
A	CYS273
A	HIS276

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 505

Chain	Residue
A	HIS170
A	CYS174
A	CYS182
A	CYS185

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 506

Chain	Residue
A	CYS289
A	CYS292
A	CYS336
A	CYS339

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN D 101

Chain	Residue
D	CYS78
D	CYS81
D	HIS93

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 501

Chain	Residue
E	HIS170
E	CYS174
E	CYS182
E	CYS185

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 502

Chain	Residue
E	HIS250
E	CYS271
E	CYS273
E	HIS276

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 503

Chain	Residue
E	CYS46
E	CYS49
E	CYS68
E	HIS73

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 504

Chain	Residue
E	CYS289
E	CYS292
E	CYS336
E	CYS339

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 505

Chain	Residue
E	CYS60
E	CYS63
E	HIS77
E	HIS83

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 506

Chain	Residue
E	CYS4
E	HIS6
E	CYS96
E	CYS99

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 101

Chain	Residue
H	CYS78
H	CYS81
H	HIS93
H	HOH203

Functional Information from PROSITE/UniProt

site_id	PS00972
Number of Residues	16
Details	USP_1 Ubiquitin specific protease (USP) domain signature 1. GLinmGNtCFMSSiLQ

Chain	Residue	Details
A	GLY138-GLN153

site_id	PS00973
Number of Residues	18
Details	USP_2 Ubiquitin specific protease (USP) domain signature 2. YeLiGIvsHkGtvne..GHY

Chain	Residue	Details
A	TYR411-TYR428

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744\|PubMed:22106047

Chain	Residue	Details
B	LYS68
E	LYS22-CYS122
F	LYS68

site_id	SWS_FT_FI2
Number of Residues	2
Details	ACT_SITE: Nucleophile

Chain	Residue	Details
A	CYS146
E	CYS146

site_id	SWS_FT_FI3
Number of Residues	2
Details	ACT_SITE: Proton acceptor => ECO:0000255\|PROSITE-ProRule:PRU10092, ECO:0000255\|PROSITE-ProRule:PRU10093

Chain	Residue	Details
A	HIS427
E	HIS427

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00502

Chain	Residue	Details
A	CYS46
E	CYS49
E	CYS60
E	CYS63
E	CYS68
E	HIS73
E	HIS77
E	HIS83
A	CYS49
A	CYS60
A	CYS63
A	CYS68
A	HIS73
A	HIS77
A	HIS83
E	CYS46

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)