2QJN | pdb_00002qjn

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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e2qjnD5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
C		e2qjnC5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
B		e2qjnB5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
A		e2qjnA5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)

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
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	IPR029065	Enolase_C-like	Unknown
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	IPR013341	Mandelate racemase, N-terminal domain	Domain
A, B, C, D	IPR034589	D-mannonate dehydratase-like	Family
A, B, C, D	IPR034587	D-mannonate dehydratase	Family
A, B, C, D	IPR013342	Mandelate racemase, C-terminal domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.