1JDI | pdb_00001jdi

CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE

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	d1jdia_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	AraD-like aldolase/epimerase	L-ribulose-5-phosphate 4-epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d1jdif_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	AraD-like aldolase/epimerase	L-ribulose-5-phosphate 4-epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d1jdie_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	AraD-like aldolase/epimerase	L-ribulose-5-phosphate 4-epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d1jdid_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	AraD-like aldolase/epimerase	L-ribulose-5-phosphate 4-epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1jdic_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	AraD-like aldolase/epimerase	L-ribulose-5-phosphate 4-epimerase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1jdib_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	AraD-like aldolase/epimerase	L-ribulose-5-phosphate 4-epimerase	(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	AraD-like aldolase/epimerase	8024544	4000777	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	AraD/HMP-PK domain-like	8036923	3001331	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	AraD/HMP-PK domain-like	8036923	3001331	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	AraD/HMP-PK domain-like	8036923	3001331	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	AraD/HMP-PK domain-like	8036923	3001331	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	AraD/HMP-PK domain-like	8036923	3001331	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	AraD/HMP-PK domain-like	8036923	3001331	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	NIR_SIR	e1jdiA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NIR_SIR	ECOD (v294.1)
F	NIR_SIR	e1jdiF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NIR_SIR	ECOD (v294.1)
E	NIR_SIR	e1jdiE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NIR_SIR	ECOD (v294.1)
D	NIR_SIR	e1jdiD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NIR_SIR	ECOD (v294.1)
C	NIR_SIR	e1jdiC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NIR_SIR	ECOD (v294.1)
B	NIR_SIR	e1jdiB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: NIR_SIR	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)
F	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)
E	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)
D	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)
C	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)
B	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00596	Class II Aldolase and Adducin N-terminal domain (Aldolase_II)	Class II Aldolase and Adducin N-terminal domain	This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE	lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity isomerase activity L-ribulose-phosphate 4-epimerase activity racemase and epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity isomerase activity L-ribulose-phosphate 4-epimerase activity racemase and epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	monosaccharide metabolic process carbohydrate metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process pentose metabolic process L-lyxose metabolic process arabinose metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process L-arabinose catabolic process monosaccharide metabolic process carbohydrate metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process pentose metabolic process L-lyxose metabolic process arabinose metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process L-arabinose catabolic process L-arabinose catabolic process to D-xylulose 5-phosphate D-xylulose 5-phosphate metabolic process L-arabinose metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036409	Class II aldolase/adducin N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050197	Aldolase class II family, sugar metabolism enzymes	Family
A, B, C, D, E A, B, C, D, E, F	IPR004661	L-ribulose-5-phosphate 4-epimerase	Family
A, B, C, D, E A, B, C, D, E, F	IPR033748	L-ribulose-5-phosphate 4-epimerase AraD	Family
A, B, C, D, E A, B, C, D, E, F	IPR001303	Class II aldolase/adducin N-terminal	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	L-ribulose-5-phosphate 4-epimerase M-CSA #273	L-ribulose-5-phosphate-4-epimerase catalyses the interconversion of L-ribulose 5-phosphate(L-Ru5P) and D-xylulose 5-phosphate(D-Xu5P). It belongs to a superfamily of epimerases/aldolases that catalyse carbon-carbon bond cleavage reactions via a metal stabilised enolate intermediate. The conversion from L-Ru5P to D-Xu5P allows bacteria to utilise arabinose as an energy source by converting it into an intermediate in the pentose phosphate pathway(D-Xu5P).	Defined by 5 residues: HIS:A-95HIS:A-97ASP:A_4-120HIS:A-171TYR:A-229 Some residues are not modelled and lack atomic coordinates. Visualization is not available. Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available. EC: 5.1.3.4 (PDB Primary Data)

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.