6YX5 | pdb_00006yx5

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

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	d6yx5a1	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	d6yx5a2	Artifacts	Tags	Tags	Tags	N-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	8089844	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	e6yx5A1	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)
B	1.10.357.170	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (utative)
B	1.20.120.1520	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (utative)

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, 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	PF20879	SidM, N-terminal domain (SidM_N)	SidM, N-terminal domain	This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consi ...	This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain (this entry), a Rab1-activation domain (Pfam:PF20851), and a C- terminal phosphatidylinositol 4-phosphate-binding (P4M) domain (Pfam:PF14860). The N-terminal is mostly alpha-helical, but also shows a short two-stranded beta-sheet [1,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ras-related protein Rab-8A	small GTPase binding protein binding binding enzyme binding GTPase binding protein tyrosine kinase binding kinase binding protein kinase binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides small GTPase binding protein binding binding enzyme binding GTPase binding protein tyrosine kinase binding kinase binding protein kinase binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity 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 GDP binding cytoskeletal protein binding myosin V binding myosin binding	protein localization cellular localization establishment of protein localization nitrogen compound transport protein localization to synapse transport neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane vesicle-mediated transport neurotransmitter receptor transport to plasma membrane localization cellular macromolecule localization regulation of biological quality protein localization to cell periphery protein localization cellular localization establishment of protein localization nitrogen compound transport protein localization to synapse transport neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane vesicle-mediated transport neurotransmitter receptor transport to plasma membrane localization cellular macromolecule localization regulation of biological quality protein localization to cell periphery protein localization to postsynaptic membrane neurotransmitter receptor transport establishment of protein localization to membrane biological regulation localization within membrane protein localization to membrane establishment of localization protein-containing complex localization vesicle-mediated transport to the plasma membrane regulation of postsynaptic membrane neurotransmitter receptor levels protein transport macromolecule localization cellular process protein localization to postsynapse protein localization to cell junction receptor localization to synapse catabolic process autophagy metabolic process process utilizing autophagic mechanism protein localization to plasma membrane multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development regulation of localization regulation of biological process regulation of cellular process regulation of protein localization regulation of transport regulation of establishment of protein localization regulation of protein transport regulation of cellular localization regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of signaling regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication vesicle-mediated transport in synapse protein localization to cilium protein localization to organelle secretion export from cell membrane docking organelle localization by membrane tethering secretion by cell exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis membrane organization membrane fusion organelle membrane fusion vesicle organization organelle fusion organelle organization Golgi vesicle fusion to target membrane vesicle fusion Golgi vesicle transport organelle assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization cell projection assembly cellular response to stimulus cellular response to nitrogen compound response to stimulus response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus regulation of catabolic process regulation of autophagy regulation of metabolic process intracellular transport endocytic recycling endosomal transport establishment of localization in cell establishment of protein localization to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane neurotransmitter receptor transport, endosome to postsynaptic membrane endosome to plasma membrane protein transport intracellular protein transport Golgi organization endomembrane system organization	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse membrane intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle Golgi apparatus endomembrane system Golgi membrane endosome membrane endosome cell body neuronal cell body transport vesicle presynapse synaptic vesicle secretory vesicle exocytic vesicle cilium ciliary basal body microtubule organizing center microtubule cytoskeleton midbody nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen centrosome centriolar satellite centriole cell periphery plasma membrane non-motile cilium nucleoplasm lytic vacuole vacuole lysosome ciliary membrane plasma membrane region cell projection membrane trans-Golgi network transport vesicle clathrin-coated vesicle coated vesicle Golgi-associated vesicle recycling endosome recycling endosome membrane Golgi apparatus subcompartment organelle subcompartment trans-Golgi network membrane trans-Golgi network ciliary base
B	Multifunctional virulence effector protein DrrA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding small GTPase binding protein binding enzyme binding GTPase binding protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups enzyme regulator activity guanyl nucleotide binding GTP binding hydrolase activity guanyl ribonucleotide binding GDP binding ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides pyrophosphatase activity GTPase activity nucleoside-triphosphatase regulator activity GTPase regulator activity guanyl-nucleotide exchange factor activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding adenylyltransferase activity AMPylase activity	regulation of molecular function regulation of catalytic activity regulation of hydrolase activity biological regulation regulation of GTPase activity protein nucleotidylation protein adenylylation macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of molecular function regulation of catalytic activity regulation of hydrolase activity biological regulation regulation of GTPase activity protein nucleotidylation protein adenylylation macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein guanylylation	cellular anatomical structure membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR050305	Small GTPase superfamily, Rab	Family
A	IPR005225	Small GTP-binding domain	Domain
A	IPR001806	Small GTPase	Family
B	IPR048718	SidM, Rab1-activation domain	Domain
B	IPR038346	DrrA, PI4P binding domain superfamily	Homologous Superfamily
B	IPR028057	DrrA phosphatidylinositol 4-phosphate binding domain	Domain
B	IPR048717	SidM, N-terminal domain	Domain
B	IPR033784	SidM, Rab1-activation domain, Legionella pneumophila	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P61006	rheumatoid arthritis astrocytic tumor plasma cell myeloma cancer psoriasis ovarian cancer

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.