Annotations: 9QGY

Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N	SCOP2B Superfamily	GBAA_5634-like	8106452	3002779	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	GBAA_5634-like	8106452	3002779	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H, I, J, K G, H, I, J, K, L	PF25876	RND MFP, alpha-helical hairpin domain (HH_MFP_RND)	RND MFP, alpha-helical hairpin domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance- nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1]. The alpha -helical hairpin domain of AcrA shows conformational flexibility, which has potential mechanistic significance in coupling between AcrA conformations and TolC channel opening [1].	Domain
G, H, I, J, K G, H, I, J, K, L	PF25917	RND MFP, barrel-sandwich hybrid domain (BSH_RND)	RND MFP, barrel-sandwich hybrid domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance-nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1]. The barrel-sandwich hybrid domain is an important structural feature found in membrane fusion proteins. This domain plays a crucial role in the assembly and function of tripartite drug efflux systems [2]. It is involved in interactions with the other components of the RND pumps.	Domain
G, H, I, J, K G, H, I, J, K, L	PF25967	RND MFPs, C-terminal permuted SH3 domain (RND-MFP_C)	RND MFPs, C-terminal permuted SH3 domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance- nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1]. Another member MexA, a Pseudomonas aeruginosa homolog of AcrA, is a component of the tripartite multidrug efflux system MexAB-OprM which is a major factor for antibiotic resistance by exporting a large variety of antimicrobial compounds [2]. The domain represented by this entry folds into an open barrel with a circularly permuted topology of SH3-like barrels. This domain is involved in interactions with efflux pump membrane transporter.	Domain
G, H, I, J, K G, H, I, J, K, L	PF25944	RND MFPs, beta-barrel domain (Beta-barrel_RND)	RND MFPs, beta-barrel domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance- nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1,2]. The domain represented in this entry folds into a six-stranded closed beta-barrel with a greek-key topology which has a structural similarity to the C-terminal domain of alanine racemase. This domain is interrupted by the barrel-sandwich hybrid domain which is inserted after the first beta-strand of the barrel. This model does not include the N-terminal strand.	Domain
D, E, F	PF12883	Protein of unknown function (DUF3828) (DUF3828)	Protein of unknown function (DUF3828)	This is a family of bacterial proteins of unknown function.	Domain
A, B, C	PF02321	Outer membrane efflux protein (OEP)	Outer membrane efflux protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M, N	Macrolide export ATP-binding/permease protein MacB	xenobiotic transmembrane transporter activity ABC-type transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type xenobiotic transporter activity transporter activity transmembrane transporter activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding xenobiotic transmembrane transporter activity ABC-type transporter activity active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type xenobiotic transporter activity transporter activity transmembrane transporter activity ATP-dependent activity 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity ATP hydrolysis 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 polymyxin transmembrane transporter activity lipid transmembrane transporter activity	response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane detoxification export from cell export across plasma membrane response to toxic substance transmembrane transport cellular process	cellular anatomical structure membrane cell periphery plasma membrane protein-containing complex transmembrane transporter complex MacAB-TolC complex membrane protein complex macrolide transmembrane transporter complex transporter complex
G, H, I, J, K G, H, I, J, K, L	Macrolide export protein MacA	polymyxin transmembrane transporter activity lipid transmembrane transporter activity transporter activity transmembrane transporter activity efflux transmembrane transporter activity identical protein binding protein binding binding	response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane response to stimulus response to chemical response to antibiotic polymyxin transport localization nitrogen compound transport transport macromolecule localization lipid localization lipid transport establishment of localization xenobiotic export from cell xenobiotic transport xenobiotic detoxification by transmembrane export across the plasma membrane detoxification export from cell export across plasma membrane response to toxic substance transmembrane transport cellular process	cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery plasma membrane MacAB-TolC complex macrolide transmembrane transporter complex extrinsic component of membrane
D, E, F	Uncharacterized lipoprotein YbjP	-	-	cell periphery cellular anatomical structure plasma membrane membrane
A, B, C	Outer membrane protein TolC	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity monoatomic ion channel activity monoatomic ion transmembrane transporter activity efflux transmembrane transporter activity identical protein binding wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity monoatomic ion channel activity monoatomic ion transmembrane transporter activity efflux transmembrane transporter activity identical protein binding protein binding binding enterobactin transmembrane transporter activity siderophore-iron transmembrane transporter activity iron chelate transmembrane transporter activity	response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process response to antibiotic response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process response to antibiotic monoatomic ion transmembrane transport monoatomic ion transport organic anion transport carboxylic acid transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport organic acid transport monocarboxylic acid transport macromolecule localization siderophore transport iron ion transport metal ion transport enterobactin transport transition metal ion transport monoatomic cation transport iron coordination entity transport xenobiotic export from cell xenobiotic detoxification by transmembrane export across the plasma membrane export from cell export across plasma membrane	cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane MacAB-TolC complex cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane MacAB-TolC complex macrolide transmembrane transporter complex cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M, N	IPR050250	Macrolide Exporter MacB	Family
M, N	IPR017871	ABC transporter-like, conserved site	Conserved Site
M, N	IPR017911	MacB-like, ATP-binding domain	Domain
M, N	IPR003838	ABC3 transporter permease, C-terminal	Domain
M, N	IPR003439	ABC transporter-like, ATP-binding domain	Domain
M, N	IPR003593	AAA+ ATPase domain	Domain
M, N	IPR025857	MacB-like periplasmic core domain	Domain
M, N	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR058627	Multidrug resistance protein MdtA-like, C-terminal permuted SH3 domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR030190	Macrolide export protein MacA, alpha-hairpin domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR006143	RND efflux pump, membrane fusion protein	Family
G, H, I, J, K G, H, I, J, K, L	IPR058625	Multidrug resistance protein MdtA-like, barrel-sandwich hybrid domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR058623	Macrolide export protein MacA	Family
G, H, I, J, K G, H, I, J, K, L	IPR058626	Multidrug resistance protein MdtA-like, beta-barrel domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR058624	Multidrug resistance protein MdtA-like, alpha-helical hairpin domain	Domain
D, E, F	IPR024289	Domain of unknown function DUF3828	Domain
A, B, C	IPR058622	Outer membrane channel protein TolC	Family
A, B, C	IPR010130	Type I secretion outer membrane protein, TolC	Family
A, B, C	IPR051906	Outer membrane protein TolC-like	Family
A, B, C	IPR003423	Outer membrane efflux protein	Family

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9QGY | pdb_00009qgy

Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage