2QJJ

Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2qjja2	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	d2qjja1	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	d2qjjb2	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	d2qjjb1	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	d2qjjc2	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	d2qjjc1	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	d2qjjd2	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	d2qjjd1	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)
A	PF02746	e2qjjA5	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: PF02746	ECOD (1.6)
A	PF13378	e2qjjA6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
B	PF02746	e2qjjB5	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: PF02746	ECOD (1.6)
B	PF13378	e2qjjB6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
C	PF02746	e2qjjC5	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: PF02746	ECOD (1.6)
C	PF13378	e2qjjC6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)
D	PF02746	e2qjjD5	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: PF02746	ECOD (1.6)
D	PF13378	e2qjjD6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF13378	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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 organic substance metabolic process catabolic process carbohydrate catabolic process primary metabolic process metabolic process organic substance catabolic 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	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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	mannonate dehydratase M-CSA #960	Characterised enzymes in the mannonate dehydratase family (manD) catalyse the dehydration of mannonate to 2-dehydro-3-deoxy-D-gluconate, as part of the catabolism of D-glucuronate. Generally, genomes that encode a member of the mannonate dehydratase family do not have a UxuA (iron(II)-dependent mannoate dehydratase) homologue. Though UxuA also has the TIM barrel fold, it is not a member of the enolase superfamily. Thus, the enolase superfamily mannonate dehydratase family and the UxuAs are an example of convergent evolution of function.	Defined by 9 residues: ARG:A-147TYR:A-159ASP:A-210HIS:A-212GLU:A-236GLU:A-262ARG:A-283GLU:A-339TRP:A-402 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.