4AMA

Crystal Structure of N-acetylneuraminic acid lyase from Staphylococcus aureus with the chemical modification thia-lysine at position 165 in complex with pyruvate

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4amaa1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
A	d4amaa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
B	d4amab1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
B	d4amab2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
C	d4amac1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
C	d4amac2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
D	d4amad_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Aldolase	8059165	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8059165	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8059165	3000445	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aldolase	8059165	3000445	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	DHDPS	e4amaA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)
B	DHDPS	e4amaB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)
C	DHDPS	e4amaC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)
D	DHDPS	e4amaD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00701	Dihydrodipicolinate synthetase family (DHDPS)	Dihydrodipicolinate synthetase family	This family has a TIM barrel structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	N-ACETYLNEURAMINATE LYASE	oxo-acid-lyase activity N-acetylneuraminate lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process catabolic process oxoacid metabolic process carbohydrate derivative metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process carboxylic acid catabolic process amino sugar metabolic process nitrogen compound metabolic process small molecule metabolic process carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process catabolic process oxoacid metabolic process carbohydrate derivative metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process carboxylic acid catabolic process amino sugar metabolic process nitrogen compound metabolic process small molecule metabolic process amide metabolic process N-acetylneuraminate metabolic process organonitrogen compound catabolic process N-acetylneuraminate catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process cellular metabolic process carboxylic acid metabolic process amino sugar catabolic process cellular process small molecule catabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005264	N-acetylneuraminate lyase	Family
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR020625	Schiff base-forming aldolase, active site	Active Site
A, B, C, D	IPR002220	DapA-like	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.