1FDY | pdb_00001fdy

N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE

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	d1fdyd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	N-acetylneuraminate lyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1fdyc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	N-acetylneuraminate lyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1fdyb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	N-acetylneuraminate lyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1fdya_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	N-acetylneuraminate lyase	(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	Aldolase	8044525	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8044525	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8044525	3000445	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aldolase	8044525	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)
D	DHDPS	e1fdyD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)
C	DHDPS	e1fdyC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)
B	DHDPS	e1fdyB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHDPS	ECOD (1.6)
A	DHDPS	e1fdyA1	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)
D	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)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	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 identical protein binding protein binding binding	carbohydrate metabolic process primary metabolic process metabolic process cellular process cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms N-acetylneuraminate catabolic process carbohydrate derivative catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process carbohydrate metabolic process primary metabolic process metabolic process cellular process cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms N-acetylneuraminate catabolic process carbohydrate derivative catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process carbohydrate derivative metabolic process organic acid catabolic process organic acid metabolic process amino sugar catabolic process carboxylic acid catabolic process amino sugar metabolic process small molecule metabolic process amide metabolic process small molecule catabolic process N-acetylneuraminate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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	IPR020624	Schiff base-forming aldolase, conserved site	Conserved Site
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

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

Chains	Enzyme Name	Description	Catalytic Residues
A	N-acetylneuraminate lyase M-CSA #553	The N-acetylneuraminate lyase (NAL) enzymes are a subfamily of the (beta/alpha)8 enzymes. They all share a common catalytic step but catalyse reactions in different biological pathways. The formation of a Schiff base between a strictly conserved lysine residue and the C2 carbon of the common keto-acid moiety of the substrate is a common feature of the group, with the NAL enzymes catalysing the aldol cleavage of N-acetylneuraminate to form N-acetylmannosine and pyruvate via the distinctive Schiff base intermediate.	Defined by 2 residues: TYR:A-137LYS:A-165 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.3.3 (PDB Primary Data) Search M-CSA Motif + EC 4.1.3.3

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.