2QJN

Crystal structure of D-mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and 2-keto-3-deoxy-D-gluconate

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)
B	d2qjnb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
B	d2qjnb1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
C	d2qjnc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
C	d2qjnc1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
A	d2qjna2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
A	d2qjna1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
D	d2qjnd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)
D	d2qjnd1	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	automated matches	automated matches	(Novosphingobium aromaticivorans ) [TaxId: 48935 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	MR_MLE_N	e2qjnB5	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: MR_MLE_N	ECOD (1.6)
B	MR_MLE_C_1	e2qjnB6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MR_MLE_C_1	ECOD (1.6)
C	MR_MLE_N	e2qjnC5	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: MR_MLE_N	ECOD (1.6)
C	MR_MLE_C_1	e2qjnC6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MR_MLE_C_1	ECOD (1.6)
A	MR_MLE_N	e2qjnA5	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: MR_MLE_N	ECOD (1.6)
A	MR_MLE_C_1	e2qjnA6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MR_MLE_C_1	ECOD (1.6)
D	MR_MLE_N	e2qjnD5	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Enolase N-terminal domain-like (From Topology)	T: Enolase N-terminal domain-like	F: MR_MLE_N	ECOD (1.6)
D	MR_MLE_C_1	e2qjnD6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MR_MLE_C_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, 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
A, B, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Mandelate racemase/muconate lactonizing enzyme	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding mannonate dehydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process metabolic process cellular process amino acid metabolic process amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR034593	D-galactonate dehydratase DgoD-like	Family
A, B, C, D	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain	Domain
A, B, C, D	IPR053379	D-mannonate dehydratase GalD subfamily	Family
A, B, C, D	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site	Conserved Site
A, B, C, D	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR034589	D-mannonate dehydratase-like	Family
A, B, C, D	IPR029065	Enolase C-terminal domain-like	Domain
A, B, C, D	IPR034587	D-mannonate dehydratase	Family
A, B, C, D	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal	Domain
A, B, C, D	IPR029017	Enolase-like, N-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.