2NUU | pdb_00002nuu

Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex

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: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2nuua2	Membrane and cell surface proteins and peptides	Ammonium transporter	Ammonium transporter	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2nuua3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2nuub2	Membrane and cell surface proteins and peptides	Ammonium transporter	Ammonium transporter	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2nuub3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2nuuc2	Membrane and cell surface proteins and peptides	Ammonium transporter	Ammonium transporter	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2nuuc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2nuud2	Membrane and cell surface proteins and peptides	Ammonium transporter	Ammonium transporter	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2nuud3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2nuue2	Membrane and cell surface proteins and peptides	Ammonium transporter	Ammonium transporter	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2nuue3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2nuuf2	Membrane and cell surface proteins and peptides	Ammonium transporter	Ammonium transporter	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2nuuf3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2nuug_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	Prokaryotic signal transducing protein	PII-homolog GlnK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2nuuh_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	Prokaryotic signal transducing protein	PII-homolog GlnK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2nuui_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	Prokaryotic signal transducing protein	PII-homolog GlnK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d2nuuj_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	Prokaryotic signal transducing protein	PII-homolog GlnK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d2nuuk_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	Prokaryotic signal transducing protein	PII-homolog GlnK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d2nuul_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	Prokaryotic signal transducing protein	PII-homolog GlnK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ammonium transporter	8040742	3001978	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ammonium transporter	8040742	3001978	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ammonium transporter	8040742	3001978	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ammonium transporter	8040742	3001978	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ammonium transporter	8040742	3001978	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ammonium transporter	8040742	3001978	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GlnB-like	8035258	3001165	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	GlnB-like	8035258	3001165	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	GlnB-like	8035258	3001165	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	GlnB-like	8035258	3001165	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	GlnB-like	8035258	3001165	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	GlnB-like	8035258	3001165	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	Ammonium_transp_1	e2nuuA1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Ammonium transporter	F: Ammonium_transp_1	ECOD (1.6)
B	Ammonium_transp_1	e2nuuB1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Ammonium transporter	F: Ammonium_transp_1	ECOD (1.6)
C	Ammonium_transp_1	e2nuuC1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Ammonium transporter	F: Ammonium_transp_1	ECOD (1.6)
D	Ammonium_transp_1	e2nuuD1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Ammonium transporter	F: Ammonium_transp_1	ECOD (1.6)
E	Ammonium_transp_1	e2nuuE1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Ammonium transporter	F: Ammonium_transp_1	ECOD (1.6)
F	Ammonium_transp_1	e2nuuF1	A: alpha complex topology	X: Ammonium transporter-related (From Homology)	H: Ammonium transporter-related	T: Ammonium transporter	F: Ammonium_transp_1	ECOD (1.6)
G	P-II	e2nuuG1	A: a+b two layers	X: Alpha-beta plaits	H: GlnB-like (From Topology)	T: GlnB-like	F: P-II	ECOD (1.6)
H	P-II	e2nuuH1	A: a+b two layers	X: Alpha-beta plaits	H: GlnB-like (From Topology)	T: GlnB-like	F: P-II	ECOD (1.6)
I	P-II	e2nuuI1	A: a+b two layers	X: Alpha-beta plaits	H: GlnB-like (From Topology)	T: GlnB-like	F: P-II	ECOD (1.6)
J	P-II	e2nuuJ1	A: a+b two layers	X: Alpha-beta plaits	H: GlnB-like (From Topology)	T: GlnB-like	F: P-II	ECOD (1.6)
K	P-II	e2nuuK1	A: a+b two layers	X: Alpha-beta plaits	H: GlnB-like (From Topology)	T: GlnB-like	F: P-II	ECOD (1.6)
L	P-II	e2nuuL1	A: a+b two layers	X: Alpha-beta plaits	H: GlnB-like (From Topology)	T: GlnB-like	F: P-II	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3430.10	Mainly Alpha	Orthogonal Bundle	Ammonium transporter fold	Ammonium transporter AmtB like domains	CATH (4.3.0)
B	1.10.3430.10	Mainly Alpha	Orthogonal Bundle	Ammonium transporter fold	Ammonium transporter AmtB like domains	CATH (4.3.0)
C	1.10.3430.10	Mainly Alpha	Orthogonal Bundle	Ammonium transporter fold	Ammonium transporter AmtB like domains	CATH (4.3.0)
D	1.10.3430.10	Mainly Alpha	Orthogonal Bundle	Ammonium transporter fold	Ammonium transporter AmtB like domains	CATH (4.3.0)
E	1.10.3430.10	Mainly Alpha	Orthogonal Bundle	Ammonium transporter fold	Ammonium transporter AmtB like domains	CATH (4.3.0)
F	1.10.3430.10	Mainly Alpha	Orthogonal Bundle	Ammonium transporter fold	Ammonium transporter AmtB like domains	CATH (4.3.0)
G	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
H	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
I	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
J	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
K	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
L	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00909	Ammonium Transporter Family (Ammonium_transp)	Ammonium Transporter Family	-	Family
G, H, I, J, K G, H, I, J, K, L	PF00543	Nitrogen regulatory protein P-II (P-II)	Nitrogen regulatory protein P-II	P-II modulates the activity of glutamine synthetase. It is a tetrameric protein encoded by the glnB gene, a component of the adenylation cascade involved in the regulation of GS activity [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Ammonia channel	ammonium channel activity passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity identical protein binding protein binding binding	transmembrane transport localization nitrogen compound transport transport ammonium transmembrane transport cellular process establishment of localization one-carbon compound transport gas transport carbon dioxide transport	cell periphery cellular anatomical structure plasma membrane membrane
G, H, I, J, K G, H, I, J, K, L	Nitrogen regulatory protein P-II 2	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 enzyme regulator activity molecular function regulator activity identical protein binding protein binding	response to nutrient levels regulation of biological process regulation of response to nutrient levels response to stimulus positive regulation of nitrogen utilization homeostatic process biological regulation positive regulation of biological process nitrogen utilization regulation of nitrogen utilization positive regulation of response to stimulus cellular homeostasis chemical homeostasis regulation of response to stimulus intracellular nitrogen homeostasis response to nutrient levels regulation of biological process regulation of response to nutrient levels response to stimulus positive regulation of nitrogen utilization homeostatic process biological regulation positive regulation of biological process nitrogen utilization regulation of nitrogen utilization positive regulation of response to stimulus cellular homeostasis chemical homeostasis regulation of response to stimulus intracellular nitrogen homeostasis intracellular chemical homeostasis positive regulation of response to nutrient levels	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR018047	Ammonium transporter, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR029020	Ammonium/urea transporter	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001905	Ammonium transporter	Family
A, B, C, D, E A, B, C, D, E, F	IPR024041	Ammonium transporter AmtB-like domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR015867	Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR011322	Nitrogen regulatory PII-like, alpha/beta	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR002187	Nitrogen regulatory protein PII	Family
G, H, I, J, K G, H, I, J, K, L	IPR002332	Nitrogen regulatory protein P-II, urydylation site	PTM
G, H, I, J, K G, H, I, J, K, L	IPR017918	Nitrogen regulatory protein PII, conserved site	Conserved Site

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Amt/Mep/Rh proteins	AmtB ammonia channel in complex with GlnK

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.