Annotations: 1CT9

CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI

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
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)
D	d1ct9d1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	Asparagine synthetase B, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1ct9d2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Asparagine synthetase B, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ct9c1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	Asparagine synthetase B, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ct9c2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Asparagine synthetase B, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ct9b1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	Asparagine synthetase B, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ct9b2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Asparagine synthetase B, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ct9a1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	Asparagine synthetase B, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ct9a2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Asparagine synthetase B, N-terminal domain	(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)
D	SCOP2B Superfamily	Class II glutamine amidotransferases	8036757	3000131	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8044208	3001593	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II glutamine amidotransferases	8036757	3000131	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8044208	3001593	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8036757	3000131	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8044208	3001593	SCOP2B (2022-06-29)
A	SCOP2 Family	Alpha subunit of glutamate synthase, GAT domain-like	8024378	4000340	SCOP2 (2022-06-29)
A	SCOP2 Family	N-type ATP pyrophosphatases	8031830	4003831	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II glutamine amidotransferases	8036757	3000131	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8044208	3001593	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	GATase_2	e1ct9D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: GATase_2	ECOD (v294.1)
D	Usp	e1ct9D2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Usp	ECOD (v294.1)
C	GATase_2	e1ct9C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: GATase_2	ECOD (v294.1)
C	Usp	e1ct9C2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Usp	ECOD (v294.1)
B	GATase_2	e1ct9B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: GATase_2	ECOD (v294.1)
B	Usp	e1ct9B2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Usp	ECOD (v294.1)
A	GATase_7	e1ct9A1	A: few secondary structure elements	X: Ntn/PP2C	H: Ntn	T: Class II glutamine amidotransferases	F: GATase_7	ECOD (v294.1)
A	Asn_synthase	e1ct9A2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains	T: HUP domains	F: Asn_synthase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	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)
C	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13537	Glutamine amidotransferase domain (GATase_7)	Glutamine amidotransferase domain	This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes such as asparagine synthetase and glutamine-fructose-6-phosphate transaminase.	Domain
A, B, C, D	PF00733	Asparagine synthase (Asn_synthase)	Asparagine synthase	This family is always found associated with Pfam:PF00310. Members of this family catalyse the conversion of aspartate to asparagine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	ASPARAGINE SYNTHETASE B	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 identical protein binding protein binding protein homodimerization activity protein dimerization activity aspartate-ammonia ligase activity acid-ammonia (or amide) ligase activity ammonia ligase activity amino acid binding	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process L-asparagine biosynthetic process oxoacid metabolic process small molecule biosynthetic process aspartate family amino acid biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process L-asparagine biosynthetic process oxoacid metabolic process small molecule biosynthetic process aspartate family amino acid biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process asparagine metabolic process proteinogenic amino acid biosynthetic process small molecule metabolic process alpha-amino acid biosynthetic process L-glutamine metabolic process catabolic process amino acid catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A, B, C, D	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B, C, D	IPR033738	Asparagine synthase, N-terminal domain	Domain
A, B, C, D	IPR006426	Asparagine synthase, glutamine-hydrolyzing	Family
A, B, C, D	IPR017932	Glutamine amidotransferase type 2 domain	Domain
A, B, C, D	IPR001962	Asparagine synthase	Domain
A, B, C, D	IPR050795	Asparagine Synthetase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	asparagine synthase (glutamine-hydrolysing) M-CSA #302	Asparagine synthetase B catalyses the ATP dependent formation of asparagine from aspartate using either glutamine or ammonia as a nitrogen source. The enzyme is a homodimer with two active sites [PMID:10587437] in each subunit, one responsible for glutamine hydrolysis and one for asparagine synthesis, separated by a hydrophobic intramolecular tunnel around 20A long [PMID:12706338]. Sequencing analysis has shown the synthetase to belong to the larger glutamine transferase family.	Defined by 6 residues: ALA:A-1LEU:A-50ASN:A-74GLY:A-75THR:A-321ARG:A-324 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 6.3.5.4 (PDB Primary Data)

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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.