3L0M

Crystal structure of Rab1-activation domain and P4M domain of SidM/DrrA from legionella

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DrrA_P4M	e3l0mA2	A: alpha arrays	X: Methane monooxygenase hydrolase gamma subunit-like	H: SidM C-terminal P4M domain (From Topology)	T: SidM C-terminal P4M domain	F: DrrA_P4M	ECOD (1.6)
A	SidM_DrrA_GEF	e3l0mA1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
B	DrrA_P4M	e3l0mB2	A: alpha arrays	X: Methane monooxygenase hydrolase gamma subunit-like	H: SidM C-terminal P4M domain (From Topology)	T: SidM C-terminal P4M domain	F: DrrA_P4M	ECOD (1.6)
B	SidM_DrrA_GEF	e3l0mB3	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
A	1.20.1280.280	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
B	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
B	1.20.1280.280	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14860	DrrA phosphatidylinositol 4-phosphate binding domain (DrrA_P4M)	DrrA phosphatidylinositol 4-phosphate binding domain	This domain binds to phosphatidylinositol 4-phosphate. It is found in Legionella pneumophila DrrA, a protein involved in the redirection of endoplasmic reticulum-derived vesicles to the Legionella-containing vacuoles [1,2].	Domain
A, 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
A, B	PF20851	SidM, Rab1-activation domain (SidM_Rab1-act)	SidM, Rab1-activation 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, a Rab1-activation domain (this entry), and a C- terminal phosphatidylinositol 4-phosphate-binding (P4M) domain (Pfam:PF14860). The Rab1-activation domain strongly interacts with Rab1 switch regions leading to substantial conformational changes on SidM binding. This domain is organized into two layers of helices [1,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DrrA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity 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 localization establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane establishment of localization protein targeting to membrane regulation of molecular function regulation of catalytic activity regulation of hydrolase activity biological regulation regulation of GTPase activity protein localization establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane establishment of localization protein targeting to membrane localization cellular macromolecule localization macromolecule localization cellular process protein nucleotidylation organic substance metabolic process organonitrogen compound metabolic process protein adenylylation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein guanylylation	membrane cellular anatomical entity 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, B	IPR048718	SidM, Rab1-activation domain	Domain
A, B	IPR038346	DrrA, PI4P binding domain superfamily	Homologous Superfamily
A, B	IPR028057	DrrA phosphatidylinositol 4-phosphate binding domain	Domain
A, B	IPR048717	SidM, N-terminal domain	Domain
A, B	IPR033784	SidM, Rab1-activation domain, Legionella pneumophila	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM				DrrA PtdIns(4) binding domain

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.