1QO0

Amide receptor of the amidase operon of Pseudomonas aeruginosa (AmiC) complexed with the negative regulator AmiR.

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1qo0a_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Amide receptor/negative regulator of the amidase operon (AmiC)	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1qo0b_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Amide receptor/negative regulator of the amidase operon (AmiC)	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C [auth D]	d1qo0d_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	Positive regulator of the amidase operon AmiR	Positive regulator of the amidase operon AmiR	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D [auth E]	d1qo0e_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	Positive regulator of the amidase operon AmiR	Positive regulator of the amidase operon AmiR	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	L-arabinose binding protein-like	8020887	4000206	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type 1 solute binding protein-like	8033267	3000125	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Type 1 solute binding protein-like	8033267	3000125	SCOP2B (2022-06-29)
C [auth D]	SCOP2 Family	Positive regulator of the amidase operon AmiR	8031672	4003653	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	CheY-like	8044050	3001156	SCOP2 (2022-06-29)
D [auth E]	SCOP2B Superfamily	CheY-like	8044050	3001156	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	Peripla_BP_6	e1qo0A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_6	ECOD (1.6)
A	Peripla_BP_5	e1qo0A3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_5	ECOD (1.6)
B	Peripla_BP_6	e1qo0B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_6	ECOD (1.6)
B	Peripla_BP_5	e1qo0B3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_5	ECOD (1.6)
C [auth D]	ANTAR	e1qo0D2	A: alpha arrays	X: RuvA-C	H: ANTAR domain (From Topology)	T: ANTAR domain	F: ANTAR	ECOD (1.6)
C [auth D]	AmiR	e1qo0D3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: AmiR	ECOD (1.6)
D [auth E]	ANTAR	e1qo0E1	A: alpha arrays	X: RuvA-C	H: ANTAR domain (From Topology)	T: ANTAR domain	F: ANTAR	ECOD (1.6)
D [auth E]	AmiR	e1qo0E2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: AmiR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C [auth D]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C [auth D]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D [auth E]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D [auth E]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13433	Periplasmic binding protein domain (Peripla_BP_5)	Periplasmic binding protein domain	This domain is found in a variety of bacterial periplasmic binding proteins.	Domain
C [auth D], D [auth E]	PF21332	AmiR, N-terminal (AmiR_N)	AmiR, N-terminal	This is the N-terminal domain of Aliphatic amidase regulator (AmiR) which acts as a transcriptional antitermination factor. It positively controls AmiE, the gene for aliphatic amidase [1].	Domain
C [auth D], D [auth E]	PF03861	ANTAR domain (ANTAR)	ANTAR domain	ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the domain consists of a coiled-coil.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	AMIC	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups amide binding binding	regulation of amide catabolic process regulation of amide metabolic process regulation of biological process catabolic process amide catabolic process biological regulation metabolic process amide metabolic process regulation of catabolic process regulation of metabolic process amino acid transport localization transport establishment of localization	-
C [auth D], D [auth E]	AMIR	RNA binding binding organic cyclic compound binding nucleic acid binding	carbon utilization response to nutrient levels response to stimulus cellular catabolic process catabolic process cellular metabolic process metabolic process cellular process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly carbon utilization response to nutrient levels response to stimulus cellular catabolic process catabolic process cellular metabolic process metabolic process cellular process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process positive regulation of cellular biosynthetic process regulation of amide catabolic process regulation of amide metabolic process amide catabolic process amide metabolic process regulation of catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B	IPR000709	Leu/Ile/Val-binding protein	Family
A, B	IPR039570	AmiC, periplasmic binding domain	Domain
C [auth D], D [auth E]	IPR011006	CheY-like superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR005561	ANTAR domain	Domain
C [auth D], D [auth E]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR049021	AmiR, N-terminal	Domain
C [auth D], D [auth E]	IPR008327	Signal transduction response regulator, antiterminator	Family

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.