4U4M | pdb_00004u4m

Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d4u4md_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4u4mc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4u4mb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4u4ma_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Glyco_hydro_31_3rd	e4u4mD1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	ECOD (v294.1)
C	Glyco_hydro_31_3rd	e4u4mC1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	ECOD (v294.1)
B	Glyco_hydro_31_3rd	e4u4mB1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	ECOD (v294.1)
A	Glyco_hydro_31_3rd	e4u4mA1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Glyco_hydro_31_3rd	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	YagE	lyase activity 2-dehydro-3-deoxy-D-gluconate aldolase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity 2-dehydro-3-deoxy-D-pentonate aldolase activity identical protein binding protein binding binding	catabolic process oxoacid metabolic process aldonic acid catabolic process carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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.