4GYP | pdb_00004gyp

Crystal structure of the heterotetrameric complex of GlucD and GlucDRP from E. coli K-12 MG1655 (EFI TARGET EFI-506058)

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4gypd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4gypd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4gypc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4gypc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4gypb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	D-glucarate dehydratase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4gypb1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	D-glucarate dehydratase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4gypa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	D-glucarate dehydratase-like	D-glucarate dehydratase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4gypa1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	D-glucarate dehydratase	(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)
B	SCOP2B Superfamily	Enolase N-terminal domain-like	8034351	3001064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Enolase C-terminal domain-like	8034350	3000476	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase N-terminal domain-like	8034351	3001064	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Enolase C-terminal domain-like	8034350	3000476	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)
D	AHSA1	e4gypD3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: AHSA1	ECOD (v294.1)
C	AHSA1	e4gypC3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: AHSA1	ECOD (v294.1)
B	ABC_tran	e4gypB2	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
A	HSP90,HATPase_c_3	e4gypA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Precorrin-8X methylmutase CbiC/CobH	T: Precorrin-8X methylmutase CbiC/CobH	F: HSP90,HATPase_c_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
C	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
B	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
A	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF02746	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain (MR_MLE_N)	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain	SCOP reports fold similarity with enolase N-terminal domain.	Domain
C, D	PF13378	Enolase C-terminal domain-like (MR_MLE_C)	Enolase C-terminal domain-like	This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N Pfam:PF02746 domain. EC:4.2.1.40.	Domain
A, B	PF13378	Enolase C-terminal domain-like (MR_MLE_C)	Enolase C-terminal domain-like	This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N Pfam:PF02746 domain. EC:4.2.1.40.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Glucarate dehydratase-related protein	hydro-lyase activity glucarate dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate metabolic process D-glucarate catabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carbohydrate catabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid catabolic process carboxylic acid catabolic process D-glucarate metabolic process carbohydrate metabolic process D-glucarate catabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carbohydrate catabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid catabolic process carboxylic acid catabolic process D-glucarate metabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process amino acid metabolic process amino acid catabolic process	-
A, B	Glucarate dehydratase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity glucarate dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity	carbohydrate metabolic process D-glucarate catabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carbohydrate catabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid catabolic process carboxylic acid catabolic process D-glucarate metabolic process carbohydrate metabolic process D-glucarate catabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carbohydrate catabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid catabolic process carboxylic acid catabolic process D-glucarate metabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR034593	D-galactonate dehydratase DgoD-like	Family
C, D	IPR029065	Enolase_C-like	Unknown
C, D	IPR034598	D-Glucarate dehydratase-like	Family
C, D	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site	Conserved Site
C, D	IPR013342	Mandelate racemase, C-terminal domain	Domain
C, D	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
C, D	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
C, D	IPR013341	Mandelate racemase, N-terminal domain	Domain
A, B	IPR034593	D-galactonate dehydratase DgoD-like	Family
A, B	IPR029065	Enolase_C-like	Unknown
A, B	IPR017653	Glucarate dehydratase	Family
A, B	IPR034598	D-Glucarate dehydratase-like	Family
A, B	IPR013342	Mandelate racemase, C-terminal domain	Domain
A, B	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A, B	IPR036849	Enolase-like, C-terminal domain superfamily	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.