4R1P | pdb_00004r1p

Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase with Mn2+

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)
F	d4r1pf2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
F	d4r1pf1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
E	d4r1pe2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
E	d4r1pe1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
D	d4r1pd2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
D	d4r1pd1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
C	d4r1pc2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
C	d4r1pc1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
B	d4r1pb2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
B	d4r1pb1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
A	d4r1pa2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
A	d4r1pa1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Peptidase_M24	e4r1pF2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (v294.1)
F	YkuD	e4r1pF3	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
E	Peptidase_M24	e4r1pE2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (v294.1)
E	YkuD	e4r1pE3	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
D	Peptidase_M24	e4r1pD1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (v294.1)
D	YkuD	e4r1pD2	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
C	Peptidase_M24	e4r1pC1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (v294.1)
C	YkuD	e4r1pC2	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
B	Peptidase_M24	e4r1pB1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (v294.1)
B	YkuD	e4r1pB2	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
A	Peptidase_M24	e4r1pA2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (v294.1)
A	YkuD	e4r1pA3	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.10940	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.40.50.10940	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.10940	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.10940	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.10940	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.10940	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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	PF11762	L-arabinose isomerase C-terminal domain (Arabinose_Iso_C)	L-arabinose isomerase C-terminal domain	This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arab ...	This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme [1]. This is a C-terminal non catalytic domain.	Domain
A, B, C, D, E A, B, C, D, E, F	PF02610	L-arabinose isomerase N-terminal domain (AraA_N)	L-arabinose isomerase N-terminal domain	This entry represents a domain found N-terminal in L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source ...	This entry represents a domain found N-terminal in L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme [1]. The domain represented by this entry is composed of a central parallel beta-sheet packed with alpha-helices on both sides and with topology similar to the topology of the middle domain [2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF24856	L-arabinose isomerase central domain (AraA_central)	L-arabinose isomerase central domain	This entry represents a domain found central in L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source af ...	This entry represents a domain found central in L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme [1]. The domain represented by this entry is composed of a central parallel beta-sheet packed with alpha-helices on both sides and with topology similar to the topology of the N-terminal domain [2].	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-arabinose isomerase	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding isomerase activity L-arabinose isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic activity	monosaccharide metabolic process arabinose metabolic process carbohydrate metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process L-arabinose catabolic process primary metabolic 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 monosaccharide metabolic process arabinose metabolic process carbohydrate metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process L-arabinose catabolic process primary metabolic 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 metabolic process cellular process small molecule metabolic process phosphorus metabolic process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose 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, E A, B, C, D, E, F	IPR009015	L-fucose isomerase, N-terminal/central domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003762	L-arabinose isomerase	Family
A, B, C, D, E A, B, C, D, E, F	IPR055390	L-arabinose isomerase, central domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038583	L-arabinose isomerase, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR055389	L-arabinose isomerase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR024664	L-arabinose isomerase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004216	L-fucose/L-arabinose isomerase, C-terminal	Homologous Superfamily

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.