4KYI

Crystal structure of the phospholipase VipD from Legionella pneumophila in complex with the human GTPase Rab5

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4kyid_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4kyib_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4kyif_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d4kyih_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	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)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8098730	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8098730	3002022	SCOP2B (2022-06-29)
F	SCOP2 Family	Ras-like monodomain GTPases	8098729	4004043	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Ras-like P-loop GTPases	8098730	3002022	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8098730	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	flgH_like	e4kyiA2	A: alpha bundles	X: ExoU toxin middle helical domain (From Topology)	H: ExoU toxin middle helical domain (From Topology)	T: ExoU toxin middle helical domain	F: flgH_like	ECOD (1.6)
A	Patatin	e4kyiA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: Patatin	ECOD (1.6)
C	flgH_like	e4kyiC2	A: alpha bundles	X: ExoU toxin middle helical domain (From Topology)	H: ExoU toxin middle helical domain (From Topology)	T: ExoU toxin middle helical domain	F: flgH_like	ECOD (1.6)
C	Patatin	e4kyiC3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: Patatin	ECOD (1.6)
E	flgH_like	e4kyiE2	A: alpha bundles	X: ExoU toxin middle helical domain (From Topology)	H: ExoU toxin middle helical domain (From Topology)	T: ExoU toxin middle helical domain	F: flgH_like	ECOD (1.6)
E	Patatin	e4kyiE3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: Patatin	ECOD (1.6)
G	flgH_like	e4kyiG2	A: alpha bundles	X: ExoU toxin middle helical domain (From Topology)	H: ExoU toxin middle helical domain (From Topology)	T: ExoU toxin middle helical domain	F: flgH_like	ECOD (1.6)
G	Patatin	e4kyiG1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: Patatin	ECOD (1.6)
D	Ras	e4kyiD1	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	e4kyiB1	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)
F	Ras	e4kyiF1	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)
H	Ras	e4kyiH1	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	3.40.1090.10	Alpha Beta	3-Layer(aba) Sandwich	Cytosolic phospholipase A2 catalytic domain	Cytosolic phospholipase A2 catalytic domain	CATH (4.3.0)
C	3.40.1090.10	Alpha Beta	3-Layer(aba) Sandwich	Cytosolic phospholipase A2 catalytic domain	Cytosolic phospholipase A2 catalytic domain	CATH (4.3.0)
E	3.40.1090.10	Alpha Beta	3-Layer(aba) Sandwich	Cytosolic phospholipase A2 catalytic domain	Cytosolic phospholipase A2 catalytic domain	CATH (4.3.0)
G	3.40.1090.10	Alpha Beta	3-Layer(aba) Sandwich	Cytosolic phospholipase A2 catalytic domain	Cytosolic phospholipase A2 catalytic domain	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
H	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, G	PF01734	Patatin-like phospholipase (Patatin)	Patatin-like phospholipase	-	Family
A, C, E, G	PF22140	VipD-like, C-terminal domain (VipD-like_C)	VipD-like, C-terminal domain	This domain is found in VipD from Legionella pneumophila (effector vacuolar protein sorting inhibitor protein D), which localises to early endosomal membranes and alters their lipid and protein composition. This process protects the pathogen from end ...	This domain is found in VipD from Legionella pneumophila (effector vacuolar protein sorting inhibitor protein D), which localises to early endosomal membranes and alters their lipid and protein composition. This process protects the pathogen from endosomal fusion. VipD adopts a two-domain fold, with a N-terminal domain homologous to patatin (Pfam:PF01734) and a C-terminal domain (this entry) that contains ten alpha-helices and two short beta-strands. VipD localises to early endosomes via this domain [1,2].	Domain
B, D, F, H	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, G	VipD	hydrolase activity catalytic activity	lipid catabolic process catabolic process metabolic process primary metabolic process lipid metabolic process	-
B, D, F, H	Ras-related protein Rab-5C	guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 GTP binding purine ribonucleoside triphosphate 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 plasma membrane to endosome transport vesicle-mediated transport import into cell endocytosis	cellular anatomical entity endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cellular anatomical entity endomembrane system vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome pigment granule intracellular vesicle melanosome cytoplasmic vesicle vesicle endosome endosome membrane early endosome early endosome membrane cytoplasmic vesicle membrane vesicle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle lipid droplet intracellular non-membrane-bounded organelle non-membrane-bounded organelle azurophil granule secretory granule primary lysosome secretory vesicle azurophil granule membrane secretory granule membrane cell periphery plasma membrane synapse transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane cell junction transport vesicle exocytic vesicle membrane exocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
A, C, E, G	IPR054392	VipD-like, C-terminal domain	Domain
A, C, E, G	IPR002641	Patatin-like phospholipase domain	Domain
A, C, E, G	IPR052580	Probable Lipid Hydrolase	Family
B, D, F, H	IPR005225	Small GTP-binding domain	Domain
B, D, F, H	IPR001806	Small GTPase	Family
B, D, F, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: P51148	colorectal cancer heart disease vitiligo glioblastoma hypothyroidism Hashimoto thyroiditis psoriasis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
B, D, F, H	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	P-loop containing nucleoside triphosphate hydrolases	Ras family

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.