3D47 | pdb_00003d47

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and D-malate

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Aminotran_1_2	e3d47A2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
A	DAO	e3d47A3	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
B	Aminotran_1_2	e3d47B2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
B	DAO	e3d47B1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
E	Aminotran_1_2	e3d47E2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
E	DAO	e3d47E3	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
F	Aminotran_1_2	e3d47F2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
F	DAO	e3d47F1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
H	Aminotran_1_2	e3d47H2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
H	DAO	e3d47H3	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
G	Aminotran_1_2	e3d47G2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
G	DAO	e3d47G3	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
D	Aminotran_1_2	e3d47D2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
D	DAO	e3d47D3	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)
C	Aminotran_1_2	e3d47C2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Aminotran_1_2	ECOD (develop294)
C	DAO	e3d47C1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (develop294)

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)
E	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
E	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
F	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
F	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
H	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
H	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
G	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
G	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	Putative galactonate dehydratase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity L-rhamnonate dehydratase 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, E A, B, C, D, E, F, G, H	IPR029065	Enolase_C-like	Unknown
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR046945	L-rhamnonate dehydratase-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013341	Mandelate racemase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013342	Mandelate racemase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029017	Enolase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023444	L-rhamnonate dehydratase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	L-rhamnonate dehydratase M-CSA #962	L-rhamnonate dehydratase is a member of the enolase superfamily that catalyses the syn dehydration of L-rhamnonate. It belongs to the mandelate racemase/muconate lactonising enzyme family, specifically the RhamD subfamily.	Defined by 6 residues: ASP:A-226GLU:A-252GLU:A-280ASP:A-302HIS:A-329GLU:A-349 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2.1.90 (UniProt) Search M-CSA Motif + EC 4.2.1.90

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.

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