7P47 | pdb_00007p47

Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth D]	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	UBC-like	8061577	3000570	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)
E [auth D]	Rad60-SLD	e7p47D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
D [auth E]	Rad60-SLD	e7p47E1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Rad60-SLD	ECOD (1.6)
C [auth A]	COG5627	e7p47A1	A: alpha bundles	X: Long alpha-hairpin	H: Endosomal sorting complex assembly domains (From Topology)	T: Endosomal sorting complex assembly domains	F: COG5627	ECOD (1.6)
C [auth A]	zf-Nse	e7p47A2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-Nse	ECOD (1.6)
B [auth C]	UQ_con	e7p47C1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E], E [auth D]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
C [auth A]	PF22326	E3 SUMO-protein ligase MMS21, N-terminal domain (MMS21_N)	E3 SUMO-protein ligase MMS21, N-terminal domain	This domain is found at the N-terminal end of E3 SUMO-protein ligase MMS21 from Saccharomyces cerevisiae and similar fungal proteins. MMS21 acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide e ...	This domain is found at the N-terminal end of E3 SUMO-protein ligase MMS21 from Saccharomyces cerevisiae and similar fungal proteins. MMS21 acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide excision repair and in repair of ionizing radiation damage. This domain forms an helix bundle with a coiled-coil structure. It is required for the binding to Smc5, which is essential for cell growth and resistance to DNA damage [1].	Domain
C [auth A]	PF11789	Zinc-finger of the MIZ type in Nse subunit (zf-Nse)	Zinc-finger of the MIZ type in Nse subunit	Nse1 and Nse2 are novel non-SMC subunits of the fission yeast Smc5-6 DNA repair complex. This family is the zinc-finger domain similar to the MIZ type of zinc-finger [1].	Domain
B [auth C]	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], E [auth D]	Ubiquitin-like protein SMT3	protein tag activity molecular tag activity protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen
C [auth A]	E3 SUMO-protein ligase MMS21	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle cell cycle process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis cellular response to stimulus double-strand break repair localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle cell cycle process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm membraneless organelle intracellular membraneless organelle chromosome membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome
B [auth C]	SUMO-conjugating enzyme UBC9	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding SUMO conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity	peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cell division peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cell division mitotic spindle elongation spindle elongation microtubule cytoskeleton organization mitotic cell cycle cellular component organization mitotic sister chromatid segregation cell cycle cellular component organization or biogenesis chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation mitotic spindle organization organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen
A [auth B]	Structural maintenance of chromosomes protein 5	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity DNA binding damaged DNA binding nucleic acid binding single-stranded DNA binding	nucleobase-containing compound metabolic process resolution of DNA recombination intermediates DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis chromosome separation nucleobase-containing compound metabolic process resolution of DNA recombination intermediates DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis chromosome separation cell cycle chromosome segregation cell cycle process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E], E [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
D [auth E], E [auth D]	IPR000626	Ubiquitin-like domain	Domain
D [auth E], E [auth D]	IPR022617	Rad60/SUMO-like domain	Domain
C [auth A]	IPR004181	Zinc finger, MIZ-type	Domain
C [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C [auth A]	IPR054753	E3 SUMO-protein ligase MMS21, N-terminal domain	Domain
C [auth A]	IPR026846	E3 SUMO-protein ligase Nse2 (Mms21)	Family
B [auth C]	IPR050113	Ubiquitin-conjugating enzyme	Family
B [auth C]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B [auth C]	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
B [auth C]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A [auth B]	IPR003395	RecF/RecN/SMC, N-terminal	Domain
A [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.