4I1O | pdb_00004i1o

Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3

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	d4i1oa1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4i1oa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4i1oc1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4i1oc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4i1oe1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4i1oe2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d4i1og1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d4i1og2	Artifacts	Tags	Tags	Tags	C-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	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	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)
A	Ras	e4i1oA1	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)
C	Ras	e4i1oC1	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)
E	Ras	e4i1oE1	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)
G	Ras	e4i1oG1	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	LepB_N	e4i1oB2	A: alpha bundles	X: LepB GAP domain N-terminal subdomain (From Topology)	H: LepB GAP domain N-terminal subdomain (From Topology)	T: LepB GAP domain N-terminal subdomain	F: LepB_N	ECOD (1.6)
B	LepB_C	e4i1oB3	A: alpha bundles	X: LepB GAP domain C-terminal subdomain (From Topology)	H: LepB GAP domain C-terminal subdomain (From Topology)	T: LepB GAP domain C-terminal subdomain	F: LepB_C	ECOD (1.6)
D	LepB_N	e4i1oD2	A: alpha bundles	X: LepB GAP domain N-terminal subdomain (From Topology)	H: LepB GAP domain N-terminal subdomain (From Topology)	T: LepB GAP domain N-terminal subdomain	F: LepB_N	ECOD (1.6)
D	LepB_C	e4i1oD3	A: alpha bundles	X: LepB GAP domain C-terminal subdomain (From Topology)	H: LepB GAP domain C-terminal subdomain (From Topology)	T: LepB GAP domain C-terminal subdomain	F: LepB_C	ECOD (1.6)
F	LepB_N	e4i1oF2	A: alpha bundles	X: LepB GAP domain N-terminal subdomain (From Topology)	H: LepB GAP domain N-terminal subdomain (From Topology)	T: LepB GAP domain N-terminal subdomain	F: LepB_N	ECOD (1.6)
F	LepB_C	e4i1oF3	A: alpha bundles	X: LepB GAP domain C-terminal subdomain (From Topology)	H: LepB GAP domain C-terminal subdomain (From Topology)	T: LepB GAP domain C-terminal subdomain	F: LepB_C	ECOD (1.6)
H	LepB_N	e4i1oH2	A: alpha bundles	X: LepB GAP domain N-terminal subdomain (From Topology)	H: LepB GAP domain N-terminal subdomain (From Topology)	T: LepB GAP domain N-terminal subdomain	F: LepB_N	ECOD (1.6)
H	LepB_C	e4i1oH3	A: alpha bundles	X: LepB GAP domain C-terminal subdomain (From Topology)	H: LepB GAP domain C-terminal subdomain (From Topology)	T: LepB GAP domain C-terminal subdomain	F: LepB_C	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)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
B	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
D	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
F	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
F	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
H	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
H	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	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, motili ...	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, D, F, H	PF18227	LepB GAP domain C-terminal subdomain (LepB_GAP_C)	LepB GAP domain C-terminal subdomain	This subdomain is found in the Rab1 GTPase-activating protein (GAP) domain of GAP LepB present in Legionella pneumophilia. LepB inactivates Rab1, a key regulator of the secretory vesicular trafficking machinery, by acting as a GTPase-activating prote ...	This subdomain is found in the Rab1 GTPase-activating protein (GAP) domain of GAP LepB present in Legionella pneumophilia. LepB inactivates Rab1, a key regulator of the secretory vesicular trafficking machinery, by acting as a GTPase-activating protein. LepB is also an antagonist of DrrA, which promotes Rab1. LepB acts by an atypical RabGAP mechanism that is reminiscent of classical GAPs. This is the C-terminal subdomain of the GAP domain and consists of an unusual fold [1].	Domain
B, D, F, H	PF18172	LepB GAP domain N-terminal subdomain (LepB_GAP_N)	LepB GAP domain N-terminal subdomain	This is a subdomain of a Rab GTPase-activating protein (GAP) effector from Legionella pneumophilia. This GAP modulates Rab enzymes that act as molecular switches in regulating vesicular transport in eukaryotic cells. This N-terminal subdomain belongs ...	This is a subdomain of a Rab GTPase-activating protein (GAP) effector from Legionella pneumophilia. This GAP modulates Rab enzymes that act as molecular switches in regulating vesicular transport in eukaryotic cells. This N-terminal subdomain belongs to the the GAP domain of the protein. The catalytic arginine finger (Arg444) is located within this sub-domain and it is the only arginine residue required for GAP activity [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Ras-related protein Rab-1B	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 binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide 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 binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process regulation of cellular process positive regulation of glycoprotein metabolic process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process regulation of primary metabolic process regulation of glycoprotein metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process regulation of cellular component organization regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport vesicle-mediated transport Golgi organization endomembrane system organization	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle Golgi membrane membrane bounding membrane of organelle organelle membrane endoplasmic reticulum-Golgi intermediate compartment membrane cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle Golgi membrane membrane bounding membrane of organelle organelle membrane endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol perinuclear region of cytoplasm phagophore assembly site membrane phagophore assembly site transport vesicle intracellular vesicle cytoplasmic vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B, D, F, H	LepB	-	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR005225	Small GTP-binding domain	Domain
A, C, E, G	IPR001806	Small GTPase	Family
A, C, E, G	IPR050227	Ras-related protein Rab	Family
A, C, E, G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F, H	IPR041585	LepB GAP domain, N-terminal subdomain	Domain
B, D, F, H	IPR040484	LepB GAP domain, C-terminal subdomain	Domain
B, D, F, H	IPR040519	LepB, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: Q9H0U4	astrocytic tumor coronary artery disease ovarian carcinoma bipolar disorder gout prostate carcinoma breast carcinoma myocardial ischemia

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.