2A9K

Crystal structure of the C3bot-NAD-RalA complex reveals a novel type of action of a bacterial exoenzyme

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
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	d2a9ka_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ras-related protein RalA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2a9kb_	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Exoenzyme c3	(Clostridium botulinum D phage ) [TaxId: 29342 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ras-like monodomain GTPases	8057251	4004043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8057252	3002022	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	Ras	e2a9kA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
B	ADPrib_exo_Tox	e2a9kB1	A: a+b complex topology	X: ADP-ribosylation (From Topology)	H: ADP-ribosylation (From Topology)	T: ADP-ribosylation	F: ADPrib_exo_Tox	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.90.176.10	Alpha Beta	Alpha-Beta Complex	Toxin ADP-ribosyltransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain
B	PF03496	ADP-ribosyltransferase exoenzyme (ADPrib_exo_Tox)	ADP-ribosyltransferase exoenzyme	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ras-related protein Ral-A	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding Edg-2 lysophosphatidic acid receptor binding protein binding signaling receptor binding endothelial differentiation G protein-coupled receptor binding G protein-coupled receptor binding GDP binding cytoskeletal protein binding myosin binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding ATPase binding	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cell division regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cell division regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization cellular localization membrane raft localization localization within membrane cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus ERBB signaling pathway regulation of cell communication positive regulation of signaling small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette chemotaxis taxis response to chemical response to external stimulus locomotion multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure protein localization establishment of protein localization establishment of protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to organelle protein localization to mitochondrion establishment of protein localization to mitochondrion positive regulation of organelle organization positive regulation of cellular component organization regulation of developmental process positive regulation of developmental process regulation of anatomical structure morphogenesis mitochondrion organization organelle fission mitochondrial fission regulation of mitochondrial fission regulation of mitochondrion organization positive regulation of mitochondrial fission regulation of localization regulation of transport secretion export from cell regulation of vesicle-mediated transport regulation of secretion regulation of secretion by cell secretion by cell exocytosis regulation of exocytosis filopodium assembly cell projection organization regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly positive regulation of cell projection organization positive regulation of filopodium assembly plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly postsynaptic neurotransmitter receptor internalization regulation of receptor internalization vesicle-mediated transport in synapse establishment of localization in cell regulation of postsynaptic neurotransmitter receptor internalization regulation of biological quality regulation of endocytosis regulation of receptor-mediated endocytosis protein-containing complex localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle anchoring junction cell junction focal adhesion cell-substrate junction cell periphery membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle anchoring junction cell junction focal adhesion cell-substrate junction cell periphery membrane plasma membrane synapse plasma membrane region synaptic membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell surface cell division site cleavage furrow intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle membrane Schaffer collateral - CA1 synapse Flemming body midbody
B	Mono-ADP-ribosyltransferase C3	pentosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity NAD+-protein ADP-ribosyltransferase activity transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005225	Small GTP-binding domain	Domain
A	IPR020849	Small GTPase, Ras-type	Family
A	IPR001806	Small GTPase	Family
B	IPR003540	ADP ribosyltransferase	Domain
B	IPR016678	Mono-ADP-ribosyltransferase C3/Edin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P11233	atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma psoriasis diabetes mellitus malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma glioblastoma malignant pancreatic neoplasm ovarian cancer primitive neuroectodermal tumor tuberculosis

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.