2YGY | pdb_00002ygy

Structure of wild type E. coli N-acetylneuraminic acid lyase in space group P21 crystal form II

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2ygyd1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
D	d2ygyd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
C	d2ygyc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
B	d2ygyb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
A	d2ygya1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
A	d2ygya2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	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	SmpA_OmlA	e2ygyD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
C	SmpA_OmlA	e2ygyC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
B	SmpA_OmlA	e2ygyB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
A	NTP_transf_2	e2ygyA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: NTP_transf_2	ECOD (v294.1)

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 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

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.