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	P2_N	e2vwtC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: P2_N	ECOD (develop294)
B	P2_N	e2vwtB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: P2_N	ECOD (develop294)
A	P2_N	e2vwtA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: P2_N	ECOD (develop294)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.