6V2C | pdb_00006v2c

Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp. Covalent acyl-enzyme intermediate and tetrahedral intermediate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6v2cd1	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Asparaginase type II	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d6v2cd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth B]	d6v2cb1	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Asparaginase type II	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth B]	d6v2cb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B [auth C]	d6v2cc1	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Asparaginase type II	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B [auth C]	d6v2cc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d6v2ca_	Alpha and beta proteins (a/b)	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Glutaminase/Asparaginase	Asparaginase type II	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Glutaminase/Asparaginase	8033474	3001625	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Glutaminase/Asparaginase	8033474	3001625	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Glutaminase/Asparaginase	8033474	3001625	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutaminase/Asparaginase	8033474	3001625	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)
D	PRK04183	e6v2cD2	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase C-terminal domain (From Topology)	H: Glutaminase/Asparaginase C-terminal domain (From Topology)	T: Glutaminase/Asparaginase C-terminal domain	F: PRK04183	ECOD (1.6)
D	Asparaginase	e6v2cD1	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase N-terminal domain (From Topology)	H: Glutaminase/Asparaginase N-terminal domain (From Topology)	T: Glutaminase/Asparaginase N-terminal domain	F: Asparaginase	ECOD (1.6)
C [auth B]	PRK04183	e6v2cB2	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase C-terminal domain (From Topology)	H: Glutaminase/Asparaginase C-terminal domain (From Topology)	T: Glutaminase/Asparaginase C-terminal domain	F: PRK04183	ECOD (1.6)
C [auth B]	Asparaginase	e6v2cB1	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase N-terminal domain (From Topology)	H: Glutaminase/Asparaginase N-terminal domain (From Topology)	T: Glutaminase/Asparaginase N-terminal domain	F: Asparaginase	ECOD (1.6)
B [auth C]	PRK04183	e6v2cC1	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase C-terminal domain (From Topology)	H: Glutaminase/Asparaginase C-terminal domain (From Topology)	T: Glutaminase/Asparaginase C-terminal domain	F: PRK04183	ECOD (1.6)
B [auth C]	Asparaginase	e6v2cC2	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase N-terminal domain (From Topology)	H: Glutaminase/Asparaginase N-terminal domain (From Topology)	T: Glutaminase/Asparaginase N-terminal domain	F: Asparaginase	ECOD (1.6)
A	PRK04183	e6v2cA1	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase C-terminal domain (From Topology)	H: Glutaminase/Asparaginase C-terminal domain (From Topology)	T: Glutaminase/Asparaginase C-terminal domain	F: PRK04183	ECOD (1.6)
A	Asparaginase	e6v2cA2	A: a/b three-layered sandwiches	X: Glutaminase/Asparaginase N-terminal domain (From Topology)	H: Glutaminase/Asparaginase N-terminal domain (From Topology)	T: Glutaminase/Asparaginase N-terminal domain	F: Asparaginase	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth B], D	PF00710	Asparaginase, N-terminal (Asparaginase)	Asparaginase, N-terminal	This is the N-terminal domain of this enzyme.	Domain
A, B [auth C], C [auth B], D	PF17763	Glutaminase/Asparaginase C-terminal domain (Asparaginase_C)	Glutaminase/Asparaginase C-terminal domain	This domain is found at the C-terminus of asparaginase enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth B], D	L-asparaginase 2	asparaginase activity amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding	catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-asparagine catabolic process carboxylic acid catabolic process small molecule metabolic process amide metabolic process amino acid catabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-asparagine catabolic process carboxylic acid catabolic process small molecule metabolic process amide metabolic process amino acid catabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process asparagine metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process L-asparagine metabolic process metabolic process cellular process small molecule catabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	cellular anatomical structure periplasmic space outer membrane-bounded periplasmic space cell envelope protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth B], D	IPR027473	L-asparaginase, C-terminal	Homologous Superfamily
A, B [auth C], C [auth B], D	IPR027475	Asparaginase/glutaminase, active site 2	Active Site
A, B [auth C], C [auth B], D	IPR036152	Asparaginase/glutaminase-like superfamily	Homologous Superfamily
A, B [auth C], C [auth B], D	IPR020827	Asparaginase/glutaminase, active site 1	Active Site
A, B [auth C], C [auth B], D	IPR037152	L-asparaginase, N-terminal domain superfamily	Homologous Superfamily
A, B [auth C], C [auth B], D	IPR040919	Asparaginase/glutaminase, C-terminal	Domain
A, B [auth C], C [auth B], D	IPR027474	L-asparaginase, N-terminal	Domain
A, B [auth C], C [auth B], D	IPR004550	L-asparaginase, type II	Family
A, B [auth C], C [auth B], D	IPR006034	Asparaginase/glutaminase-like	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B [auth C], C [auth B], D	AEI	Parent Component: THR RESID: AA0525 PSI-MOD : O-(L-isoaspartyl)-L-threonine (active site intermediate) MOD:01671 , O-(L-isoaspartyl)-L-threonine (cross-link) MOD:01947
A, B [auth C], C [auth B], D	QNY	Parent Component: Thr RESID: AA0525

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.