1P1X

Comparison of class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase determined at 0.99 Angstrom resolution

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)
A	d1p1xa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Deoxyribose-phosphate aldolase DeoC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1p1xb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I aldolase	Deoxyribose-phosphate aldolase DeoC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1p1xb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A	SCOP2 Family	Class I aldolase	8025658	4003216	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aldolase	8038037	3000445	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8038037	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)
A	DeoC_1	e1p1xA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
B	DeoC_1	e1p1xB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01791	DeoC/LacD family aldolase (DeoC)	DeoC/LacD family aldolase	This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function, ...	This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function, see examples Swiss:Q57843 and Swiss:P76143. The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Deoxyribose-phosphate aldolase	deoxyribose-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process deoxyribose phosphate catabolic process deoxyribose phosphate metabolic process organophosphate metabolic process 2-deoxyribose 1-phosphate catabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process deoxyribose phosphate catabolic process deoxyribose phosphate metabolic process organophosphate metabolic process 2-deoxyribose 1-phosphate catabolic process 2-deoxyribose 1-phosphate metabolic process phosphate-containing compound metabolic process metabolic process phosphorus metabolic process carbohydrate metabolic process carbohydrate catabolic process primary metabolic process nucleoside phosphate metabolic process deoxyribonucleotide catabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process nucleotide catabolic process nucleobase-containing small molecule interconversion	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023649	Deoxyribose-phosphate aldolase type II	Family
A, B	IPR002915	DeoC/FbaB/LacD aldolase	Family
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR011343	Deoxyribose-phosphate aldolase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	deoxyribose-phosphate aldolase M-CSA #613	The class I aldolase Deoxyribose-5-phosphate aldolase from Escherichia coli is able to catalyse the formation of DRP from acetaldehyde and glyceraldehyde-3-phosphate. As such is it a rare form of class I aldolase as it is able to catalyse the condensation between two aldehydes rather than an aldehyde and a ketone.	Defined by 3 residues: ASP:A-103 [auth A-102]LYS:A-168 [auth A-167]LYS:A-202 [auth A-201] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.2.4 (PDB Primary Data) Search M-CSA Motif + EC 4.1.2.4

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.