6CVL | pdb_00006cvl

Crystal structure of the Escherichia coli ATPgS-bound MetNI methionine ABC transporter in complex with its MetQ binding protein

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth B]	d6cvlb_	Membrane and cell surface proteins and peptides	MetI-like	MetI-like	MetI-like	D-methionine transport system permease protein MetI	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B [auth A]	d6cvla_	Membrane and cell surface proteins and peptides	MetI-like	MetI-like	MetI-like	D-methionine transport system permease protein MetI	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d6cvld1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	ABC transporter ATPase domain-like	Methionine import ATP-binding protein MetN	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d6cvld2	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	NIL domain-like	Methionine import ATP-binding protein MetN	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d6cvld3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A [auth C]	d6cvlc1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	ABC transporter ATPase domain-like	Methionine import ATP-binding protein MetN	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A [auth C]	d6cvlc2	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	NIL domain-like	Methionine import ATP-binding protein MetN	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A [auth C]	d6cvlc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2 Family	Phosphate binding protein-like	8058943	4000229	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Type 2 solute binding protein-like	8058944	3000083	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	MetI-like	8058246	3001716	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	MetI-like	8058246	3001716	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8018379	3002020	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ACT-like	8018383	3000006	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8018379	3002020	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	ACT-like	8018383	3000006	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)
E	Lipoprotein_9_2nd	e6cvlE2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lipoprotein_9_2nd	ECOD (1.6)
E	Lipoprotein_9_1st	e6cvlE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lipoprotein_9_1st	ECOD (1.6)
C [auth B]	BPD_transp_1	e6cvlB1	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type I ABC importer transmembrane domain fold (From Topology)	T: Type I ABC importer transmembrane domain fold	F: BPD_transp_1	ECOD (1.6)
B [auth A]	BPD_transp_1	e6cvlA1	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type I ABC importer transmembrane domain fold (From Topology)	T: Type I ABC importer transmembrane domain fold	F: BPD_transp_1	ECOD (1.6)
D	NIL	e6cvlD1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NIL	ECOD (1.6)
D	ABC_tran	e6cvlD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
A [auth C]	NIL	e6cvlC1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NIL	ECOD (1.6)
A [auth C]	ABC_tran	e6cvlC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C [auth B]	1.10.3720.10	Mainly Alpha	Orthogonal Bundle	MetI-like fold	MetI-like	CATH (4.3.0)
B [auth A]	1.10.3720.10	Mainly Alpha	Orthogonal Bundle	MetI-like fold	MetI-like	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)
D	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)
A [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth C]	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF03180	NlpA lipoprotein (Lipoprotein_9)	NlpA lipoprotein	-	Family
B [auth A], C [auth B]	PF00528	Binding-protein-dependent transport system inner membrane component (BPD_transp_1)	Binding-protein-dependent transport system inner membrane component	-	Family
A [auth C], D	PF09383	NIL domain (NIL)	NIL domain	This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conse ...	This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family.	Domain
A [auth C], D	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	MetQ periplasmic binding protein	-	import into cell organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport import across plasma membrane amino acid transmembrane transport methionine transport methionine import across plasma membrane establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport import into cell organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport import across plasma membrane amino acid transmembrane transport methionine transport methionine import across plasma membrane establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport localization sulfur amino acid transport sulfur compound transport cellular process amino acid import across plasma membrane D-methionine transmembrane transport D-amino acid transport	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope periplasmic space methionine-importing ABC transporter complex methionine-importing complex
B [auth A], C [auth B]	MetI transmembrane subunit	methionine transmembrane transporter activity D-amino acid transmembrane transporter activity ABC-type amino acid transporter activity sulfur amino acid transmembrane transporter activity sulfur compound transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type D-methionine transporter activity carboxylic acid transmembrane transporter activity ATP-dependent activity ATPase-coupled carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity active transmembrane transporter activity ABC-type transporter activity transporter activity methionine transmembrane transporter activity D-amino acid transmembrane transporter activity ABC-type amino acid transporter activity sulfur amino acid transmembrane transporter activity sulfur compound transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type D-methionine transporter activity carboxylic acid transmembrane transporter activity ATP-dependent activity ATPase-coupled carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity active transmembrane transporter activity ABC-type transporter activity transporter activity transmembrane transporter activity L-amino acid transmembrane transporter activity L-methionine transmembrane transporter activity	import into cell organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport import across plasma membrane amino acid transmembrane transport methionine transport methionine import across plasma membrane establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport import into cell organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport import across plasma membrane amino acid transmembrane transport methionine transport methionine import across plasma membrane establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport localization sulfur amino acid transport sulfur compound transport cellular process amino acid import across plasma membrane D-methionine transmembrane transport D-amino acid transport	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex methionine-importing ABC transporter complex methionine-importing complex
A [auth C], D	MetN nucleotide-binding subunit	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 L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity methionine transmembrane transporter activity sulfur amino acid transmembrane transporter activity sulfur compound transmembrane transporter activity L-methionine transmembrane transporter activity transporter activity carboxylic acid transmembrane transporter activity transmembrane transporter activity D-amino acid transmembrane transporter activity ABC-type amino acid transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity ABC-type D-methionine transporter activity ATP-dependent activity ATPase-coupled carboxylic acid transmembrane transporter activity active transmembrane transporter activity ABC-type transporter 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	import into cell organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport import across plasma membrane amino acid transmembrane transport methionine transport methionine import across plasma membrane establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport import into cell organic anion transport nitrogen compound transport carboxylic acid transmembrane transport carboxylic acid transport transport import across plasma membrane amino acid transmembrane transport methionine transport methionine import across plasma membrane establishment of localization organic cation transport transmembrane transport organic acid transport amino acid transport localization sulfur amino acid transport sulfur compound transport cellular process amino acid import across plasma membrane D-methionine transmembrane transport D-amino acid transport	cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex Gram-negative-bacterium-type cell wall external encapsulating structure cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex Gram-negative-bacterium-type cell wall external encapsulating structure cell envelope cell wall peptidoglycan-based cell wall methionine-importing ABC transporter complex methionine-importing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR004872	Lipoprotein NlpA family	Family
B [auth A], C [auth B]	IPR000515	ABC transporter type 1, transmembrane domain MetI-like	Domain
B [auth A], C [auth B]	IPR035906	MetI-like superfamily	Homologous Superfamily
B [auth A], C [auth B]	IPR051322	Amino Acid ABC Transporter Permease	Family
A [auth C], D	IPR017871	ABC transporter-like, conserved site	Conserved Site
A [auth C], D	IPR045865	ACT-like domain	Homologous Superfamily
A [auth C], D	IPR041701	Methionine import ATP-binding protein MetN, ATP-binding domain	Domain
A [auth C], D	IPR003439	ABC transporter-like, ATP-binding domain	Domain
A [auth C], D	IPR012692	ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria	Family
A [auth C], D	IPR003593	AAA+ ATPase domain	Domain
A [auth C], D	IPR018449	NIL domain	Domain
A [auth C], D	IPR050086	Methionine import ATP-binding protein MetN-like	Family
A [auth C], D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth C], B [auth A], C [auth B], D, E	OPM	Transmembrane	Alpha-helical polytopic	ABC transporters	Binding-protein-dependent transport system

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth C], B [auth A], C [auth B], D, E	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth C], B [auth A], C [auth B], D, E	MemProtMD	Annotated as membrane protein by MemProtMD

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.