MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
2.3.2.23	Transferases; Acyltransferases; Aminoacyltransferases; E2 ubiquitin-conjugating enzyme
2.3.2.24	Transferases; Acyltransferases; Aminoacyltransferases; (E3-independent) E2 ubiquitin-conjugating enzyme

Structure

PDB	Resolution (Å)	PDB name
1UR6		NMR based structural model of the UbcH5B-CNOT4 complex
1W4U		NMR solution structure of the ubiquitin conjugating enzyme UbcH5B
2CLW	1.945	Crystal structure of human ubiquitin-conjugating enzyme UbcH5B
2ESK	1.36	Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
2ESO	1.5	Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP	1.52	Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
2ESQ	1.44	Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
3A33	2.2	UbcH5b~Ubiquitin Conjugate
3JVZ	3.3	E2~Ubiquitin-HECT
3JW0	3.1	E2~Ubiquitin-HECT
3L1Y	1.6	Crystal structure of human UBC4 E2 conjugating enzyme
3TGD	1.8	Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b
3ZNI	2.21	Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex
4A49	2.214	Structure of phosphoTyr371-c-Cbl-UbcH5B complex
4A4B	2.789	Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex
4A4C	2.704	Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex
4AUQ	2.176	Structure of BIRC7-UbcH5b-Ub complex.
4DDG	3.2987	Crystal structure of human OTUB1/UbcH5b~Ub/Ub
4DDI	3.802	Crystal structure of human OTUB1/UbcH5b~Ub/Ub
4LDT	1.901	The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
4V3K	2.04	RNF38-UbcH5B-UB complex
4V3L	1.53	RNF38-UB-UbcH5B-Ub complex
4WZ3	2.7	Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2
5D0K	2.65	Structure of UbE2D2:RNF165:Ub complex
5D0M	1.913	Structure of UbE2D2:RNF165:Ub complex
5D1K	1.78	Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7
5D1L	1.618	Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
5D1M	1.581	Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
5EDV	3.48	Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex
5MNJ	2.16	Structure of MDM2-MDMX-UbcH5B-ubiquitin complex
5ULF	1.8	Crystal Structure of a UbcH5b~Ub conjugate
5ULH	1.95	Structure of RNF165 in complex with a UbcH5b~Ub conjugate
5ULK	2.38	Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate
5VZW	2.278	TRIM23 RING domain in complex with UbcH5-Ub
5ZBU	3.2	Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub
6HPR	1.7	Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
6M2C	2.702	Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain
6SQO	1.41	Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
6SQR	2.18	Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub
6SQS	1.83	Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub
6TTU	3.7	Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2
6W7Z	1.8	RNF12 RING domain in complex with Ube2d2
6W9D	3.19	RNF12 RING domain in complex with a Ube2d2~Ub conjugate
7AI0	1.559	Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1)
7AI1	2.07	Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2)
7BOL	1.797	ubiquitin-conjugating enzyme, Ube2D2
7R71	2.8	Crystal Structure of the UbArk2C-UbcH5b~Ub complex

GO term

GO ontology	GO term	GO description
Biological Process	GO:0070936	protein K48-linked ubiquitination
Biological Process	GO:0051865	protein autoubiquitination
Biological Process	GO:0036211	protein modification process
Biological Process	GO:0000209	protein polyubiquitination
Biological Process	GO:0016567	protein ubiquitination
Biological Process	GO:0006511	ubiquitin-dependent protein catabolic process
Molecular Function	GO:0005524	ATP binding
Molecular Function	GO:0061631	ubiquitin conjugating enzyme activity
Molecular Function	GO:0061630	ubiquitin protein ligase activity
Molecular Function	GO:0031625	ubiquitin protein ligase binding
Molecular Function	GO:0004842	ubiquitin-protein transferase activity
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0070062	extracellular exosome
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0032991	protein-containing complex
Cellular Component	GO:0000151	ubiquitin ligase complex

InterPro / Pfam

InterPro	InterPro name
IPR000608	Ubiquitin-conjugating enzyme E2
IPR016135	Ubiquitin-conjugating enzyme/RWD-like
IPR023313	Ubiquitin-conjugating enzyme, active site

Pfam	Pfam name
PF00179	Ubiquitin-conjugating enzyme

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1234176	Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha	Leaf	R-HSA-8953897	Cellular responses to stimuli
R-HSA-168927	TICAM1, RIP1-mediated IKK complex recruitment	Leaf	R-HSA-168256	Immune System
R-HSA-202424	Downstream TCR signaling	Leaf	R-HSA-168256	Immune System
R-HSA-2871837	FCERI mediated NF-kB activation	Leaf	R-HSA-168256	Immune System
R-HSA-5357905	Regulation of TNFR1 signaling	Leaf	R-HSA-162582	Signal Transduction
R-HSA-5607764	CLEC7A (Dectin-1) signaling	Internal node	R-HSA-168256	Immune System
R-HSA-8866652	Synthesis of active ubiquitin: roles of E1 and E2 enzymes	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-8866654	E3 ubiquitin ligases ubiquitinate target proteins	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-8951664	Neddylation	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-9033241	Peroxisomal protein import	Internal node	R-HSA-9609507	Protein localization
R-HSA-936440	Negative regulators of DDX58/IFIH1 signaling	Leaf	R-HSA-168256	Immune System
R-HSA-937041	IKK complex recruitment mediated by RIP1	Leaf	R-HSA-168256	Immune System
R-HSA-9705462	Inactivation of CSF3 (G-CSF) signaling	Leaf	R-HSA-168256	Immune System
R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation	Leaf	R-HSA-168256	Immune System

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	Medium	Approved
bone marrow	hematopoietic cells	Medium	Approved
breast	adipocytes	Low	Approved
breast	glandular cells	Medium	Approved
breast	myoepithelial cells	Low	Approved
caudate	neuronal cells	Low	Approved
cerebellum	cells in granular layer	Low	Approved
cerebral cortex	neuronal cells	Low	Approved
cerebral cortex	neuropil	Low	Approved
cervix	glandular cells	Low	Approved
colon	glandular cells	Medium	Approved
endometrium 1	glandular cells	Low	Approved
endometrium 2	glandular cells	Low	Approved
epididymis	glandular cells	Low	Approved
fallopian tube	glandular cells	Medium	Approved
gallbladder	glandular cells	Medium	Approved
hippocampus	glial cells	Low	Approved
hippocampus	neuronal cells	Medium	Approved
kidney	cells in tubules	Medium	Approved
liver	cholangiocytes	Medium	Approved
lung	macrophages	Medium	Approved
lymph node	germinal center cells	Low	Approved
lymph node	non-germinal center cells	Low	Approved
oral mucosa	squamous epithelial cells	Low	Approved
ovary	follicle cells	Low	Approved
pancreas	pancreatic endocrine cells	Low	Approved
parathyroid gland	glandular cells	Low	Approved
placenta	decidual cells	Medium	Approved
placenta	trophoblastic cells	Medium	Approved
prostate	glandular cells	Low	Approved
rectum	glandular cells	Low	Approved
seminal vesicle	glandular cells	Medium	Approved
skeletal muscle	myocytes	Medium	Approved
skin 1	Langerhans	Medium	Approved
skin 1	fibroblasts	Medium	Approved
skin 1	keratinocytes	Medium	Approved
skin 1	melanocytes	Low	Approved
skin 2	epidermal cells	Low	Approved
soft tissue 1	fibroblasts	Low	Approved
soft tissue 1	peripheral nerve	Low	Approved
soft tissue 2	fibroblasts	Low	Approved
spleen	cells in white pulp	Medium	Approved
stomach 1	glandular cells	Low	Approved
stomach 2	glandular cells	Low	Approved
testis	Leydig cells	Low	Approved
testis	cells in seminiferous ducts	Low	Approved
thyroid gland	glandular cells	Low	Approved
tonsil	germinal center cells	Low	Approved
tonsil	non-germinal center cells	Low	Approved
urinary bladder	urothelial cells	Medium	Approved

Summary of P62837

Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
Protein: Ubiquitin-conjugating enzyme E2 D2

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P62837

Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B Protein: Ubiquitin-conjugating enzyme E2 D2

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
Protein: Ubiquitin-conjugating enzyme E2 D2