2QJJ | pdb_00002qjj

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	MR_MLE_N	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: MR_MLE_N	ECOD (1.6)
A	MR_MLE_C_1	e2qjjA6	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)
B	MR_MLE_N	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: MR_MLE_N	ECOD (1.6)
B	MR_MLE_C_1	e2qjjB6	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	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: MR_MLE_N	ECOD (1.6)
C	MR_MLE_C_1	e2qjjC6	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	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: MR_MLE_N	ECOD (1.6)
D	MR_MLE_C_1	e2qjjD6	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)
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 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	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	IPR053379	D-mannonate_dehydratase_GalD	Unknown
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 EC: 4.2.1.8 (UniProt) Search M-CSA Motif + EC 4.2.1.8

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.