3L3P

Crystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Novel E3 ligase (NEL), C-terminal domain-like	8050056	4006749	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Novel E3 ligase (NEL), C-terminal domain -like	8052846	3002145	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	NEL	e3l3pA1	A: alpha arrays	X: Novel E3 ligase (NEL) (From Topology)	H: Novel E3 ligase (NEL) (From Topology)	T: Novel E3 ligase (NEL)	F: NEL	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1270.130	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	1.20.58.360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	1.20.58.90	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14496	C-terminal novel E3 ligase, LRR-interacting (NEL)	C-terminal novel E3 ligase, LRR-interacting	This NEL or novel E3 ligase domain is found at the C-terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process. At the N-terminus o ...	This NEL or novel E3 ligase domain is found at the C-terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process. At the N-terminus of the family-members there is a series of LRR repeats, and the NEL domain interacts with the most N-terminal repeat. The key residue for the ligation step is the cysteine, eg found at position 386 in UniProtKB:E7K2H2. The LRR section sequesters this active site until invasion has occurred [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	IpaH9.8	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 identical protein binding protein binding binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated perturbation of host defense response response to host defenses catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host process symbiont-mediated suppression of host defenses symbiont-mediated suppression of host inflammatory response response to host response to external biotic stimulus symbiont-mediated perturbation of host inflammatory response modulation of process of another organism protein polyubiquitination protein K27-linked ubiquitination 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 cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of biological process regulation of cellular process signaling biological regulation canonical NF-kappaB signal transduction intracellular signal transduction cell communication symbiont-mediated perturbation of host NF-kappaB cascade intracellular signaling cassette cellular process signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade protein autoubiquitination symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated perturbation of host innate immune response proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	extracellular region cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle host cell cytoplasm host cell cytosol host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR051071	Leucine-rich repeat-containing bacterial E3 ubiquitin ligases	Family
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR032674	LRR-containing bacterial E3 ligase, N-terminal	Domain
A	IPR029487	Novel E3 ligase domain	Domain

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.