2VWT | pdb_00002vwt

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex

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)
C	d2vwtc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2vwtb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2vwta_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	(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)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8078843	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8078843	3000510	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8078843	3000510	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)
C	HpcH_HpaI	e2vwtC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HpcH_HpaI	ECOD (1.6)
B	HpcH_HpaI	e2vwtB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HpcH_HpaI	ECOD (1.6)
A	HpcH_HpaI	e2vwtA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HpcH_HpaI	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF03328	HpcH/HpaI aldolase/citrate lyase (HpcH_HpaI)	HpcH/HpaI aldolase/citrate lyase	This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding transition metal ion binding nickel cation binding lyase activity catalytic activity carbon-carbon lyase activity 2-keto-3-deoxy-L-rhamnonate aldolase activity aldehyde-lyase activity 2-dehydro-3-deoxy-D-gluconate aldolase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding transition metal ion binding nickel cation binding lyase activity catalytic activity carbon-carbon lyase activity 2-keto-3-deoxy-L-rhamnonate aldolase activity aldehyde-lyase activity 2-dehydro-3-deoxy-D-gluconate aldolase activity identical protein binding protein binding	cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C	IPR023593	2-keto-3-deoxy-L-rhamnonate aldolase	Family
A, B, C	IPR005000	HpcH/HpaI aldolase/citrate lyase domain	Domain
A, B, C	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C	IPR050251	HpcH/HpaI aldolase	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.