4IRU

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	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	LepB_N	e4iruA3	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)
A	LepB_C	e4iruA4	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)
C	LepB_N	e4iruC3	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)
C	LepB_C	e4iruC4	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)
E	LepB_N	e4iruE3	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)
E	LepB_C	e4iruE4	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	Ras	e4iruF1	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	Ras	e4iruB1	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)
D	Ras	e4iruD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
A	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
C	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E	1.20.120.1700	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
E	1.25.40.830	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	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
A, C, E	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
B, D, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	LepB	-	-	membrane cellular anatomical entity
B, D, F	Ras-related protein Rab-1A	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 cell adhesion molecule binding cadherin binding protein 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	virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process organonitrogen compound metabolic 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 organic substance metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process establishment of organelle localization vesicle cytoskeletal trafficking vesicle localization cellular localization organelle transport along microtubule transport establishment of vesicle localization intracellular transport establishment of localization vesicle transport along microtubule localization organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process import into cell endocytosis vesicle-mediated transport cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport cell migration cell motility biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus multicellular organismal process regulation of cellular process positive regulation of interleukin-8 production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production regulation of multicellular organismal process positive regulation of cellular process regulation of biosynthetic process regulation of cellular metabolic process interleukin-8 production gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of interleukin-8 production protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport establishment of melanosome localization cellular pigmentation pigment granule transport establishment of pigment granule localization pigmentation pigment granule localization melanosome transport melanosome localization membrane organization vesicle budding from membrane vesicle cargo loading vesicle organization COPII-coated vesicle cargo loading COPII-coated vesicle budding signaling hormone secretion cell communication peptide secretion secretion by cell amide transport signal release regulation of biological quality growth hormone secretion secretion regulation of hormone levels cell-cell signaling export from cell peptide transport peptide hormone secretion hormone transport Golgi organization endomembrane system organization	cellular anatomical entity endomembrane system membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome cellular anatomical entity endomembrane system membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol early endosome endosome Golgi apparatus Golgi membrane membrane bounding membrane of organelle organelle membrane transport vesicle transport vesicle membrane cytoplasmic vesicle membrane vesicle membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F	Pharos: P62820	atrial fibrillation lung cancer myopathy pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia large cell medulloblastoma medulloblastoma osteosarcoma plasma cell myeloma lung adenocarcinoma metabolic syndrome X ovarian cancer Sjogren syndrome

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.