1MB9 | pdb_00001mb9

BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1mb9a1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	beta-Lactam synthetase	(Streptomyces clavuligerus ) [TaxId: 1901 ],	SCOPe (2.08)
A	d1mb9a2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	beta-Lactam synthetase	(Streptomyces clavuligerus ) [TaxId: 1901 ],	SCOPe (2.08)
B	d1mb9b1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	beta-Lactam synthetase	(Streptomyces clavuligerus ) [TaxId: 1901 ],	SCOPe (2.08)
B	d1mb9b2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	beta-Lactam synthetase	(Streptomyces clavuligerus ) [TaxId: 1901 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Class II glutamine amidotransferases	8037014	3000131	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8037013	3001593	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8037013	3001593	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8037014	3000131	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		e1mb9A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GATase_2	F:	ECOD (20:10:01)
A		e1mb9A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: SNO, Peptidase_S51	F:	ECOD (20:10:01)
B		e1mb9B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GATase_2	F:	ECOD (20:10:01)
B		e1mb9B2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: SNO, Peptidase_S51	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	BETA-LACTAM SYNTHETASE	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 carbon-nitrogen ligase activity, with glutamine as amido-N-donor asparagine synthase (glutamine-hydrolyzing) activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity (carboxyethyl)arginine beta-lactam-synthase activity cyclo-ligase activity cation binding metal ion binding	clavulanic acid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process lactam biosynthetic process carboxylic acid biosynthetic process lactam metabolic process biosynthetic process small molecule metabolic process metabolic process cellular process clavulanic acid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process lactam biosynthetic process carboxylic acid biosynthetic process lactam metabolic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A, B	IPR017932	Glutamine amidotransferase type 2 domain	Domain
A, B	IPR001962	Asparagine synthase	Domain
A, B	IPR050795	Asparagine Synthetase	Family
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	(carboxyethyl)arginine beta-lactam-synthase M-CSA #303	Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine [PMID: 11551215]. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a synthetase domain. It forms part of the pathway for the biosythesis of the beta-lactamase inhibitor clavulanate in Streptomyces clavuligerus. This entry represents the reaction occuring in the synthetase domain in which the L-N2-(2-carboxyethyl)arginine is first converted into an acyl-AMP by reaction with ATP and loss of diphosphate, and that the beta-lactam ring is then formed by the intramolecular attack of the beta-nitrogen on the activated carboxy group [PMID:9689037].	Defined by 3 residues: TYR:A-348GLU:A-382LYS:A-443 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.3.3.4 (UniProt) Search M-CSA Motif + EC 6.3.3.4

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.