6K1G | pdb_00006k1g

Crystal structure of the L-fucose isomerase soaked with Mn2+ from Raoultella sp.

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	d6k1gf2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
F	d6k1gf1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	L-fucose isomerase, N-terminal and second domains	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
E	d6k1ge2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
E	d6k1ge1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	L-fucose isomerase, N-terminal and second domains	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
D	d6k1gd2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
D	d6k1gd1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	L-fucose isomerase, N-terminal and second domains	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
C	d6k1gc2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
C	d6k1gc1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	L-fucose isomerase, N-terminal and second domains	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
B	d6k1gb2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
B	d6k1gb1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	L-fucose isomerase, N-terminal and second domains	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
A	d6k1ga2	All beta proteins	Reductase/isomerase/elongation factor common domain	FucI/AraA C-terminal domain-like	automated matches	automated matches	(Raoultella planticola ) [TaxId: 575 ],	SCOPe (2.08)
A	d6k1ga1	Alpha and beta proteins (a/b)	FucI/AraA N-terminal and middle domains	FucI/AraA N-terminal and middle domains	L-fucose isomerase, N-terminal and second domains	automated matches	(Raoultella planticola ) [TaxId: 575 ],	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	Fucose_iso_C	e6k1gF2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Fucose_iso_C	ECOD (1.6)
F	Fucose_iso_N1	e6k1gF1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N1	ECOD (1.6)
F	Fucose_iso_N2	e6k1gF3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N2	ECOD (1.6)
E	Fucose_iso_C	e6k1gE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Fucose_iso_C	ECOD (1.6)
E	Fucose_iso_N1	e6k1gE2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N1	ECOD (1.6)
E	Fucose_iso_N2	e6k1gE3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N2	ECOD (1.6)
D	Fucose_iso_C	e6k1gD3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Fucose_iso_C	ECOD (1.6)
D	Fucose_iso_N1	e6k1gD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N1	ECOD (1.6)
D	Fucose_iso_N2	e6k1gD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N2	ECOD (1.6)
C	Fucose_iso_C	e6k1gC2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Fucose_iso_C	ECOD (1.6)
C	Fucose_iso_N1	e6k1gC3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N1	ECOD (1.6)
C	Fucose_iso_N2	e6k1gC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N2	ECOD (1.6)
B	Fucose_iso_C	e6k1gB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Fucose_iso_C	ECOD (1.6)
B	Fucose_iso_N1	e6k1gB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N1	ECOD (1.6)
B	Fucose_iso_N2	e6k1gB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N2	ECOD (1.6)
A	Fucose_iso_C	e6k1gA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Fucose_iso_C	ECOD (1.6)
A	Fucose_iso_N1	e6k1gA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N1	ECOD (1.6)
A	Fucose_iso_N2	e6k1gA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: L-fucose isomerase, N-terminal and second domains	F: Fucose_iso_N2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.1070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
F	3.40.275.10	Alpha Beta	3-Layer(aba) Sandwich	L-fucose Isomerase	Chain A, domain 2	CATH (utative)
F	3.20.14.10	Alpha Beta	Alpha-Beta Barrel	L-fucose Isomerase	Chain A, domain 3	CATH (utative)
E	3.40.50.1070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
E	3.40.275.10	Alpha Beta	3-Layer(aba) Sandwich	L-fucose Isomerase	Chain A, domain 2	CATH (utative)
E	3.20.14.10	Alpha Beta	Alpha-Beta Barrel	L-fucose Isomerase	Chain A, domain 3	CATH (utative)
D	3.40.50.1070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
D	3.40.275.10	Alpha Beta	3-Layer(aba) Sandwich	L-fucose Isomerase	Chain A, domain 2	CATH (utative)
D	3.20.14.10	Alpha Beta	Alpha-Beta Barrel	L-fucose Isomerase	Chain A, domain 3	CATH (utative)
C	3.40.50.1070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
C	3.40.275.10	Alpha Beta	3-Layer(aba) Sandwich	L-fucose Isomerase	Chain A, domain 2	CATH (utative)
C	3.20.14.10	Alpha Beta	Alpha-Beta Barrel	L-fucose Isomerase	Chain A, domain 3	CATH (utative)
B	3.40.50.1070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
B	3.40.275.10	Alpha Beta	3-Layer(aba) Sandwich	L-fucose Isomerase	Chain A, domain 2	CATH (utative)
B	3.20.14.10	Alpha Beta	Alpha-Beta Barrel	L-fucose Isomerase	Chain A, domain 3	CATH (utative)
A	3.40.50.1070	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	3.40.275.10	Alpha Beta	3-Layer(aba) Sandwich	L-fucose Isomerase	Chain A, domain 2	CATH (utative)
A	3.20.14.10	Alpha Beta	Alpha-Beta Barrel	L-fucose Isomerase	Chain A, domain 3	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF07881	L-fucose isomerase, first N-terminal domain (Fucose_iso_N1)	L-fucose isomerase, first N-terminal domain	The members of this family are similar to L-fucose isomerase expressed by E. coli (Swiss:P11552, EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cle ...	The members of this family are similar to L-fucose isomerase expressed by E. coli (Swiss:P11552, EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta-sheets with surrounding alpha helices. Domain 1 demonstrates the beta-alpha-beta-alpha- beta Rossman fold. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues, and domain 1 from the adjacent subunit contributing some other residues [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF07882	L-fucose isomerase, second N-terminal domain (Fucose_iso_N2)	L-fucose isomerase, second N-terminal domain	The members of this family are similar to L-fucose isomerase expressed by E. coli (Swiss:P11552, EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol clea ...	The members of this family are similar to L-fucose isomerase expressed by E. coli (Swiss:P11552, EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF02952	L-fucose isomerase, C-terminal domain (Fucose_iso_C)	L-fucose isomerase, C-terminal domain	L-fucose isomerase (5.3.1.25) converts the aldose L-fucose into the corresponding ketose L-fuculose during the first step in fucose metabolism using Mn2+ as a cofactor. The enzyme is a hexamer, forming the largest structurally known ketol isomerase, ...	L-fucose isomerase (5.3.1.25) converts the aldose L-fucose into the corresponding ketose L-fuculose during the first step in fucose metabolism using Mn2+ as a cofactor. The enzyme is a hexamer, forming the largest structurally known ketol isomerase, and each protomer consists of three domains. This entry represents the C-terminal domain.	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-fucose isomerase	isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity arabinose isomerase activity catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding L-fucose isomerase activity	monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process fucose metabolic process L-fucose metabolic process fucose catabolic process L-fucose catabolic process small molecule metabolic process metabolic process cellular process monosaccharide metabolic process carbohydrate metabolic process catabolic process hexose catabolic process carbohydrate catabolic process hexose metabolic process primary metabolic process fucose metabolic process L-fucose metabolic process fucose catabolic process L-fucose catabolic process small molecule metabolic process metabolic process cellular process monosaccharide catabolic process small molecule catabolic process arabinose metabolic process arabinose catabolic process D-arabinose catabolic process pentose metabolic process pentose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR038393	L-fucose isomerase, domain 3 superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005763	L-fucose isomerase	Family
A, B, C, D, E A, B, C, D, E, F	IPR012889	L-fucose isomerase, N-terminal-2	Domain
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	IPR012888	L-fucose isomerase, N-terminal-1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015888	L-fucose isomerase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038391	L-fucose isomerase, domain 1 superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038392	L-fucose isomerase, domain 2 superfamily	Homologous Superfamily
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.