3V62 | pdb_00003v62

Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3v62b1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E	d3v62e1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d3v62a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d3v62d_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	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)
B	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8036430	3000780	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA clamp	8036430	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	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)
B	SmpA_OmlA	e3v62B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)
E	SmpA_OmlA	e3v62E1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)
A	EF-hand_1, EF-hand_7	e3v62A1	A: alpha bundles	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (develop294)
D	EF-hand_1, EF-hand_7	e3v62D1	A: alpha bundles	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
E	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
B, E	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
A, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	ATP-dependent DNA helicase SRS2	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 DNA binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity 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 nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity 3'-5' DNA helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA macromolecular conformation isomerase activity	cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination DNA damage response regulation of response to stimulus metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process protein-DNA complex organization cellular component organization cellular component disassembly DNA recombinase disassembly protein-containing complex organization protein-DNA complex disassembly protein-containing complex disassembly cellular component organization or biogenesis sexual reproduction reproductive process meiotic cell cycle organelle fission meiotic cell cycle process nuclear division organelle organization meiosis I meiosis I cell cycle process meiotic nuclear division cell cycle cell cycle process DNA protection double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B, E	Proliferating cell nuclear antigen	DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding	cellular process cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process cellular process cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process leading strand elongation cellular response to stimulus response to stimulus DNA damage tolerance cellular response to stress DNA damage response response to stress mismatch repair sexual reproduction reproductive process meiotic cell cycle meiotic cell cycle process meiotic mismatch repair meiosis I cell cycle process cell cycle process DNA repair translesion synthesis nucleobase-containing compound biosynthetic process macromolecule biosynthetic process error-free translesion synthesis DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization gene expression regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process mitotic sister chromatid cohesion establishment of mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion organelle organization mitotic cell cycle process establishment of sister chromatid cohesion regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress regulation of DNA repair regulation of response to stimulus maintenance of DNA repeat elements maintenance of DNA trinucleotide repeats subtelomeric heterochromatin formation nucleotide-excision repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
A, 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR014017	UvrD-like helicase, C-terminal	Domain
C, F	IPR000212	UvrD-like helicase	Family
C, F	IPR014016	UvrD-like helicase, ATP-binding domain	Domain
C, F	IPR013986	DExx box DNA helicase domain superfamily	Homologous Superfamily
C, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, E	IPR046938	DNA clamp superfamily	Homologous Superfamily
B, E	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
B, E	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
B, E	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
B, E	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
A, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, D	IPR000626	Ubiquitin-like domain	Domain
A, D	IPR022617	Rad60/SUMO-like domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.