6M2C | pdb_00006m2c

Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6m2ca1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6m2ca2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6m2cb1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6m2cb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6m2cc1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6m2cc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6m2cd1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6m2cd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	UBC-like	8040137	3000570	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBC-like	8040137	3000570	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBC-like	8040137	3000570	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	UBC-like	8040137	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	Omp85	e6m2cE1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
F	Omp85	e6m2cF1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
G	Omp85	e6m2cG1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
H	Omp85	e6m2cH1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
A	HHH_8	e6m2cA1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: HHH_8	ECOD (develop294)
B	Omp85	e6m2cB1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
C	Omp85	e6m2cC1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
D	Omp85	e6m2cD1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F, G, H	PF13920	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_3)	Zinc finger, C3HC4 type (RING finger)		Domain
A, B, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Mitochondrial ubiquitin ligase activator of NFKB 1	p53 binding protein binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity SUMO transferase activity ubiquitin protein ligase binding p53 binding protein binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity SUMO transferase activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling regulation of protein sumoylation regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein stability regulation of biological quality protein stabilization protein destabilization regulation of cellular component organization regulation of developmental process negative regulation of mitochondrial fusion negative regulation of biological process cellular component organization negative regulation of cellular process anatomical structure development regulation of mitochondrial fusion cellular component organization or biogenesis mitochondrial fusion regulation of anatomical structure morphogenesis mitochondrion organization developmental process negative regulation of cellular component organization negative regulation of developmental process regulation of organelle organization organelle fusion anatomical structure morphogenesis organelle organization negative regulation of organelle organization regulation of mitochondrion organization regulation of mitochondrial membrane potential regulation of membrane potential regulation of type I interferon-mediated signaling pathway response to cytokine response to biotic stimulus interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process immune response response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress innate immune response response to external biotic stimulus cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway immune system process type I interferon-mediated signaling pathway negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response regulation of localization transport apoptotic mitochondrial changes mitochondrial outer membrane permeabilization involved in programmed cell death localization positive regulation of mitochondrial membrane permeability involved in apoptotic process positive regulation of mitochondrial membrane permeability positive regulation of membrane permeability regulation of mitochondrial membrane permeability regulation of transport cell death establishment of localization apoptotic signaling pathway regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process apoptotic process mitochondrial outer membrane permeabilization programmed cell death cellular response to nitrogen compound cellular response to dsRNA cellular response to exogenous dsRNA response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus catabolic process regulation of type 2 mitophagy macroautophagy positive regulation of type 2 mitophagy autophagy regulation of autophagy positive regulation of autophagy of mitochondrion mitophagy regulation of autophagy of mitochondrion positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy type 2 mitophagy autophagy of mitochondrion protein ubiquitination chemokine (C-C motif) ligand 5 production multicellular organismal process negative regulation of chemokine production negative regulation of chemokine (C-C motif) ligand 5 production cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process chemokine production regulation of chemokine (C-C motif) ligand 5 production regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process protein polyubiquitination mitochondrion localization organelle localization positive regulation of organelle organization positive regulation of cellular component organization positive regulation of developmental process organelle fission mitochondrial fission regulation of mitochondrial fission positive regulation of mitochondrial fission regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of defense response to virus regulation of defense response to virus by host response to virus negative regulation of defense response to virus by host defense response to virus negative regulation of defense response to virus regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of developmental growth system development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of dendrite extension cellular developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis neurogenesis dendrite extension neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth positive regulation of growth neuron development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex mitochondrial membrane membrane protein complex organelle outer membrane organelle envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane protein-containing complex mitochondrial membrane membrane protein complex organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial protein-containing complex TOM complex outer mitochondrial membrane protein complex mitochondrial envelope mitochondrial outer membrane mitochondrial outer membrane translocase complex outer membrane organelle membrane peroxisome microbody somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection
A, B, C, D	Ubiquitin-conjugating enzyme E2 D2	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 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 ubiquitin-like protein ligase activity ubiquitin protein ligase activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein K48-linked ubiquitination protein autoubiquitination	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR051652	MDM2/MDM4 and MUL1	Family
E, F, G, H	IPR022170	E3 Ubiquitin ligase MUL1-like	Domain
E, F, G, H	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
E, F, G, H	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, B, C, D	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, B, C, D	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P62837	astrocytic tumor esophageal squamous cell carcinoma malignant ependymoma osteosarcoma atypical teratoid rhabdoid tumor glioblastoma malignant glioma ovarian cancer breast cancer large cell medulloblastoma malignant mesothelioma plasma cell myeloma

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.