2RD5 | pdb_00002rd5

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana

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	d2rd5a_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d2rd5b_	Alpha and beta proteins (a/b)	Carbamate kinase-like	Carbamate kinase-like	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d2rd5c_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d2rd5d_	Alpha and beta proteins (a+b)	Ferredoxin-like	GlnB-like	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-acetyl-l-glutamate kinase	8084035	4002449	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Carbamate kinase-like	8084036	3001310	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Carbamate kinase-like	8084036	3001310	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GlnB-like	8074421	3001165	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GlnB-like	8074421	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		e2rd5A1	A: Profilin-like	X: sensor domains	H: sensor domains	T: Glyco_hydro_16, SKN1_KRE6_Sbg1	F:	ECOD (20:10:01)
B		e2rd5B1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T:	F:	ECOD (20:10:01)
C		e2rd5C1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T:	F:	ECOD (20:10:01)
D		e2rd5D2	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
B	3.40.1160.10	Alpha Beta	3-Layer(aba) Sandwich	Carbamate kinase	Acetylglutamate kinase-like	CATH (4.3.0)
C	3.30.70.120	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	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	PF00696	Amino acid kinase family (AA_kinase)	Amino acid kinase family	-	Family
C, D	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	Acetylglutamate kinase-like protein	kinase activity acetylglutamate kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding kinase activity acetylglutamate kinase activity phosphotransferase activity, carboxyl group as acceptor transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 cation binding organic acid binding amino acid binding carboxylic acid binding arginine binding	L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process arginine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process alpha-amino acid biosynthetic process L-arginine biosynthetic process via ornithine	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast cytosol intracellular membraneless organelle plastid thylakoid membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast cytosol intracellular membraneless organelle plastid thylakoid chloroplast thylakoid membraneless organelle thylakoid
C, D	PII protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding enzyme regulator activity acetylglutamate kinase regulator activity molecular function regulator activity kinase regulator activity	regulation of cellular process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of biosynthetic process regulation of biological process fatty acid metabolic process regulation of cellular process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of biosynthetic process regulation of biological process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process biological regulation carboxylic acid metabolic process primary metabolic process fatty acid biosynthetic process regulation of ketone metabolic process biosynthetic process regulation of fatty acid biosynthetic process regulation of fatty acid metabolic process metabolic process cellular process regulation of lipid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process lipid metabolic process response to nutrient levels regulation of response to nutrient levels response to stimulus homeostatic process nitrogen utilization regulation of nitrogen utilization cellular homeostasis chemical homeostasis regulation of response to stimulus intracellular nitrogen homeostasis intracellular chemical homeostasis anthocyanin-containing compound biosynthetic process pigment metabolic process flavonoid metabolic process anthocyanin-containing compound metabolic process flavonoid biosynthetic process pigment biosynthetic process L-arginine biosynthetic process regulation of arginine biosynthetic process amino acid metabolic process regulation of amino acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-arginine biosynthetic process via ornithine arginine metabolic process regulation of amino acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process regulation of arginine biosynthetic process via ornithine alpha-amino acid biosynthetic process response to light stimulus response to radiation response to abiotic stimulus response to carbohydrate response to sucrose response to disaccharide response to chemical response to oxygen-containing compound	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle cytosol intracellular membraneless organelle plastid thylakoid chloroplast thylakoid membraneless organelle thylakoid membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle cytosol intracellular membraneless organelle plastid thylakoid chloroplast thylakoid membraneless organelle thylakoid chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004662	Acetylglutamate kinase family	Family
A, B	IPR001048	Aspartate/glutamate/uridylate kinase	Domain
A, B	IPR037528	Acetylglutamate kinase ArgB	Family
A, B	IPR001057	Glutamate/acetylglutamate kinase	Family
A, B	IPR041727	N-Acetyl-L-glutamate kinase, cyclic	Family
A, B	IPR036393	Acetylglutamate kinase-like superfamily	Homologous Superfamily
C, D	IPR015867	Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal	Homologous Superfamily
C, D	IPR011322	Nitrogen regulatory PII-like, alpha/beta	Homologous Superfamily
C, D	IPR002187	Nitrogen regulatory protein PII	Family
C, D	IPR017918	Nitrogen regulatory protein PII, conserved site	Conserved Site

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.