4WA6 | pdb_00004wa6

Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4wa6f_	All alpha proteins	Sus1-like	Sus1-like	Sus1-like	Sus1	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4wa6b_	All alpha proteins	Sus1-like	Sus1-like	Sus1-like	Sus1	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	SUS1/ENY2-like	8052552	3002127	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SUS1/ENY2-like	8052552	3002127	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	KOG4140	e4wa6H1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: KOG4140	ECOD (1.6)
D [auth E]	KOG4140	e4wa6E1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: KOG4140	ECOD (1.6)
G	Sgf11_1	e4wa6G1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: Sgf11_1	ECOD (1.6)
C	Sgf11_1	e4wa6C1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: Sgf11_1	ECOD (1.6)
F	EnY2	e4wa6F1	A: alpha duplicates or obligate multimers	X: YheA/YmcA-like	H: Protein SUS1 (From Topology)	T: Protein SUS1	F: EnY2	ECOD (1.6)
B	EnY2	e4wa6B1	A: alpha duplicates or obligate multimers	X: YheA/YmcA-like	H: Protein SUS1 (From Topology)	T: Protein SUS1	F: EnY2	ECOD (1.6)
E [auth D]	UCH	e4wa6D1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
E [auth D]	zf-UBP	e4wa6D2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-UBP	ECOD (1.6)
A	UCH	e4wa6A2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
A	zf-UBP	e4wa6A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-UBP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.246.140	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
B	1.10.246.140	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
E [auth D]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
E [auth D]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E], H	PF18508	Zinc finger domain (zf_C2H2_13)	Zinc finger domain	The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a ...	The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the zinc finger (ZnF)-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. Sgf73 contributes to maintaining both the organization and ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity. This domain is a Sgf73 fragment in the DUB module. It is a zinc finger (ZnF) domain whose integrity is essential for the incorporation of this subunit into DUBm as well as for the catalytic activity of Ubp8, as either a short deletion or point mutations in Sgf73 zinc-coordinating residues disrupt the association of Sgf73 with the rest of the DUBm [1 -4].	Domain
C, G	PF18519	SAGA-associated factor 11 N-terminal domain (Sgf11_N)	SAGA-associated factor 11 N-terminal domain	The SAGA (Spt-Ada-Gcn5-Acetyltransferase) transcriptional co-activator is a protein complex that regulates inducible yeast genes by performing multiple functions including acetylating core histones, recruiting the RNA polymerase II preinitiation comp ...	The SAGA (Spt-Ada-Gcn5-Acetyltransferase) transcriptional co-activator is a protein complex that regulates inducible yeast genes by performing multiple functions including acetylating core histones, recruiting the RNA polymerase II preinitiation complex, and deubiquitinating histone H2B. The deubiquitinating activity of SAGA resides in a distinct sub-complex called the deubiquitinating module (DUBm), which consists of four proteins that are conserved across eukaryotes: Ubp8, Sgf11, Sus1 and Sgf73. The DUBm proteins are organized into two lobes around the globular domains of Ubp8 [1]. In SAGA, Sus1 binds to Sgf11 by wrapping around this N-terminal domain of Sgf11, forming a stable dimer [2-4].	Domain
C, G	PF08209	Sgf11 (transcriptional regulation protein) (Sgf11)	Sgf11 (transcriptional regulation protein)	-	Family
B, F	PF10163	Transcription factor e(y)2 (EnY2)	Transcription factor e(y)2	-	Family
A, E [auth D]	PF02148	Zn-finger in ubiquitin-hydrolases and other protein (zf-UBP)	Zn-finger in ubiquitin-hydrolases and other protein		Domain
A, E [auth D]	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], H	SAGA-associated factor 73	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity structural molecule activity	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization metabolic process macromolecule metabolic process regulation of localization regulation of biological process protein localization to chromatin regulation of protein localization biological regulation protein localization to chromosome protein localization to organelle regulation of protein localization to chromatin intracellular protein localization ribonucleoprotein complex biogenesis protein-RNA complex assembly protein-RNA complex organization RITS complex assembly regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process transcription preinitiation complex assembly positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of DNA-templated transcription initiation positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process RNA polymerase II preinitiation complex assembly regulation of RNA polymerase II transcription preinitiation complex assembly positive regulation of cellular component organization regulation of cellular component organization positive regulation of DNA-templated transcription positive regulation of biological process protein-DNA complex organization positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA polymerase II transcription preinitiation complex assembly positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II protein-DNA complex assembly regulation of cellular component biogenesis DNA-templated transcription initiation positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II regulation of transport regulation of nucleocytoplasmic transport regulation of cellular localization regulation of intracellular transport chromatin organization chromatin remodeling	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex cytoplasm cytosol SLIK (SAGA-like) complex
C, G	SAGA-associated factor 11	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular component organization chromatin organization cellular process cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex
B, F	Transcription and mRNA export factor SUS1	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport poly(A)+ mRNA export from nucleus intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization cellular process metabolic process macromolecule metabolic process regulation of localization regulation of biological process regulation of protein localization biological regulation intracellular protein localization establishment of protein localization protein transport transcription elongation by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II 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 macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular component organization organelle organization chromosome organization cellular component organization or biogenesis transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery catabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA surveillance RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process nuclear RNA surveillance nuclear-transcribed mRNA catabolic process negative regulation of metabolic process nuclear mRNA surveillance mRNA metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process chromatin organization	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex endomembrane system organelle envelope nuclear envelope nuclear pore transcription export complex 2 cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex P-body membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen SLIK (SAGA-like) complex
A, E [auth D]	Ubiquitin carboxyl-terminal hydrolase 8	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process protein deubiquitination protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal regulation of cellular process regulation of primary metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process proteolysis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure DUBm complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle catalytic complex peptidase complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex membraneless organelle protein acetyltransferase complex SAGA-type complex SAGA complex intracellular protein-containing complex SLIK (SAGA-like) complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E], H	IPR037804	SAGA-associated factor 73	Family
D [auth E], H	IPR013243	SCA7 domain	Domain
D [auth E], H	IPR041251	SAGA-associated factor 73, zinc finger domain	Domain
C, G	IPR041216	Yeast SAGA-associated factor 11, N-terminal domain	Domain
C, G	IPR013246	SAGA complex, Sgf11 subunit	Family
B, F	IPR018783	Transcription factor, enhancer of yellow 2	Family
B, F	IPR038212	Transcription factor EnY2 superfamily	Homologous Superfamily
A, E [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, E [auth D]	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, E [auth D]	IPR001607	Zinc finger, UBP-type	Domain
A, E [auth D]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, E [auth D]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, E [auth D]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, E [auth D]	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family

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.