3SY2 | pdb_00003sy2

Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	UBC-like	8034823	3000570	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBC-like	8034823	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)
D	Acetyltransf_1	e3sy2D2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acetyltransf_1	ECOD (develop294)
C	SmpA_OmlA	e3sy2C1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)
B	zf-MYND	e3sy2B1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: zf-MYND	ECOD (develop294)
A	SNase	e3sy2A1	A: alpha bundles	X: Long alpha-hairpin	H: C-terminal UvrC-binding domain of UvrB	T: C-terminal UvrC-binding domain of UvrB	F: SNase	ECOD (develop294)
A	Ribosomal_L27	e3sy2A2	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Ribosomal_L27	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
C	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
B	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	CATH (4.3.0)
B	1.25.40.300	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Putative secreted effector protein	CATH (4.3.0)
B	3.40.1850.10	Alpha Beta	3-Layer(aba) Sandwich	HECT-like ubiquitin ligase fold	HECT-like ubiquitin ligase	CATH (4.3.0)
B	1.10.4140.10	Mainly Alpha	Orthogonal Bundle	effector protein (NleL) fold	effector protein (NleL)	CATH (4.3.0)
A	2.160.20.80	Mainly Beta	3 Solenoid	Pectate Lyase C-like	E3 ubiquitin-protein ligase SopA	CATH (4.3.0)
A	1.25.40.300	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Putative secreted effector protein	CATH (4.3.0)
A	3.40.1850.10	Alpha Beta	3-Layer(aba) Sandwich	HECT-like ubiquitin ligase fold	HECT-like ubiquitin ligase	CATH (4.3.0)
A	1.10.4140.10	Mainly Alpha	Orthogonal Bundle	effector protein (NleL) fold	effector protein (NleL)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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
A, B	PF13979	SopA-like catalytic domain (SopA_C)	SopA-like catalytic domain	This domain is found in the E. coli Type III secretion effector proteins SopA and NleL [1,2]. These proteins have been shown to act as E3 ubiquitin ligase enzymes. This domain contains the active site cysteine residue.	Domain
A, B	PF13981	SopA-like central domain (SopA)	SopA-like central domain	This domain is found in the E. coli Type III secretion effector proteins SopA and NleL [1,2]. These proteins have been shown to act as E3 ubiquitin ligase enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Ubiquitin-conjugating enzyme E2 L3	ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding nucleic acid 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 ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cell cycle phase transition cell cycle cell cycle process cell population proliferation cellular response to stimulus response to lipid response to stimulus macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cell cycle phase transition cell cycle cell cycle process cell population proliferation cellular response to stimulus response to lipid response to stimulus response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus cellular response to hormone stimulus regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein polyubiquitination RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription protein K11-linked ubiquitination response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus response to corticosteroid	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex
A, B	E3 ubiquitin-protein ligase SopA	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity	primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	host cellular component cellular anatomical structure host cell other organism part extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
C, D	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
C, D	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C, D	IPR050113	Ubiquitin-conjugating enzyme E2-like	Family
A, B	IPR025726	E3 ubiquitin ligase SopA-like central domain	Domain
A, B	IPR038270	SopA-like, catalytic domain superfamily	Homologous Superfamily
A, B	IPR025725	E3 ubiquitin-protein ligase SopA-like, catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P68036	Crohn disease juvenile idiopathic arthritis chronic hepatitis B virus infection atypical teratoid rhabdoid tumor myositis psoriasis tuberculosis celiac disease hepatitis B virus infection lung cancer osteosarcoma systemic lupus erythematosus inflammatory bowel disease malignant mesothelioma ovarian cancer Crohn disease juvenile idiopathic arthritis chronic hepatitis B virus infection atypical teratoid rhabdoid tumor myositis psoriasis tuberculosis celiac disease hepatitis B virus infection lung cancer osteosarcoma systemic lupus erythematosus inflammatory bowel disease malignant mesothelioma ovarian cancer systemic sclerosis

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.