6U7L

2.75 Angstrom Crystal Structure of Galactarate Dehydratase from Escherichia coli.

External Resource: Annotation

Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.130.110	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (utative)
D	2.30.130.110	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20629	D-galactarate/Altronate dehydratase, C-terminal (GD_AH_C)	D-galactarate/Altronate dehydratase, C-terminal	This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: t ...	This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: the N-terminal SAF domain (Pfam:PF08666) connected to the second domain (Pfam:PF04295) through a long linker and the C-terminal domain which represents the core of the protein. This domain adopts a variant of a Rossmann fold with an unusual crossover, consisting of seven-stranded parallel beta-sheets surrounded by nine alpha-helices [1]. This domain may contain a catalytic metal binding site [1].	Domain
A, B	PF04295	D-galactarate dehydratase/Altronate hydrolase, second domain (GD_AH_second)	D-galactarate dehydratase/Altronate hydrolase, second domain	This entry includes D-galactarate dehydratase (GarD, EC:4.2.1.42) which catalyses the reaction D-galactarate = 5-keto-4-deoxy-D glucarate + H2O, [1] and altronate hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyses D-altronate = 2-keto-2 ...	This entry includes D-galactarate dehydratase (GarD, EC:4.2.1.42) which catalyses the reaction D-galactarate = 5-keto-4-deoxy-D glucarate + H2O, [1] and altronate hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyses D-altronate = 2-keto-2- deoxygluconate + H2O [2]. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core [3]. GarD structure revealed that it is a dimer in solution; each monomer has three domains, an N-terminal SAF domain (Pfam:PF08666), a second domain represented in this entry and a C-terminal domain [5]. This domain consists of three parallel beta-strands, surrounded by three alpha-helices and it interacts with the C-terminal domain from the second chain to form a dimerisation surface [5].	Domain
A, B	PF08666	SAF domain (SAF)	SAF domain	This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.	Domain
C, D	PF20629	D-galactarate/Altronate dehydratase, C-terminal (GD_AH_C)	D-galactarate/Altronate dehydratase, C-terminal	This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: t ...	This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: the N-terminal SAF domain (Pfam:PF08666) connected to the second domain (Pfam:PF04295) through a long linker and the C-terminal domain which represents the core of the protein. This domain adopts a variant of a Rossmann fold with an unusual crossover, consisting of seven-stranded parallel beta-sheets surrounded by nine alpha-helices [1]. This domain may contain a catalytic metal binding site [1].	Domain
C, D	PF04295	D-galactarate dehydratase/Altronate hydrolase, second domain (GD_AH_second)	D-galactarate dehydratase/Altronate hydrolase, second domain	This entry includes D-galactarate dehydratase (GarD, EC:4.2.1.42) which catalyses the reaction D-galactarate = 5-keto-4-deoxy-D glucarate + H2O, [1] and altronate hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyses D-altronate = 2-keto-2 ...	This entry includes D-galactarate dehydratase (GarD, EC:4.2.1.42) which catalyses the reaction D-galactarate = 5-keto-4-deoxy-D glucarate + H2O, [1] and altronate hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyses D-altronate = 2-keto-2- deoxygluconate + H2O [2]. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core [3]. GarD structure revealed that it is a dimer in solution; each monomer has three domains, an N-terminal SAF domain (Pfam:PF08666), a second domain represented in this entry and a C-terminal domain [5]. This domain consists of three parallel beta-strands, surrounded by three alpha-helices and it interacts with the C-terminal domain from the second chain to form a dimerisation surface [5].	Domain
C, D	PF08666	SAF domain (SAF)	SAF domain	This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Galactarate dehydratase (L-threo-forming)	hydro-lyase activity galactarate dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding hydro-lyase activity galactarate dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	galactarate catabolic process galactarate metabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid metabolic process cellular catabolic process aldaric acid catabolic process carboxylic acid catabolic process small molecule metabolic process galactarate catabolic process galactarate metabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid metabolic process cellular catabolic process aldaric acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process monosaccharide metabolic process D-galacturonate catabolic process carbohydrate catabolic process monocarboxylic acid catabolic process D-galacturonate metabolic process galacturonate metabolic process carbohydrate metabolic process uronic acid metabolic process primary metabolic process monocarboxylic acid metabolic process monosaccharide catabolic process galacturonate catabolic process	-
C, D	Galactarate dehydratase (L-threo-forming)	hydro-lyase activity galactarate dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding hydro-lyase activity galactarate dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	galactarate catabolic process galactarate metabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid metabolic process cellular catabolic process aldaric acid catabolic process carboxylic acid catabolic process small molecule metabolic process galactarate catabolic process galactarate metabolic process catabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process aldaric acid metabolic process cellular catabolic process aldaric acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process monosaccharide metabolic process D-galacturonate catabolic process carbohydrate catabolic process monocarboxylic acid catabolic process D-galacturonate metabolic process galacturonate metabolic process carbohydrate metabolic process uronic acid metabolic process primary metabolic process monocarboxylic acid metabolic process monosaccharide catabolic process galacturonate catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR052172	UxaA family altronate/galactarate dehydratases	Family
A, B	IPR032893	Galactarate dehydratase (L-threo-forming) GarD, Enterobacteriaceae	Family
A, B	IPR007392	D-galactarate/Altronate dehydratase, second domain	Domain
A, B	IPR048332	D-galactarate/Altronate dehydratase, C-terminal domain	Domain
A, B	IPR013974	SAF domain	Domain
A, B	IPR044144	UxaA/GarD, SAF domain	Domain
A, B	IPR017654	Galactarate dehydratase GarD-like	Family
C, D	IPR052172	UxaA family altronate/galactarate dehydratases	Family
C, D	IPR032893	Galactarate dehydratase (L-threo-forming) GarD, Enterobacteriaceae	Family
C, D	IPR007392	D-galactarate/Altronate dehydratase, second domain	Domain
C, D	IPR048332	D-galactarate/Altronate dehydratase, C-terminal domain	Domain
C, D	IPR013974	SAF domain	Domain
C, D	IPR044144	UxaA/GarD, SAF domain	Domain
C, D	IPR017654	Galactarate dehydratase GarD-like	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	MSE	Parent Component: MET
A, B	PHD	Parent Component: ASP RESID: AA0033 PSI-MOD : L-aspartic 4-phosphoric anhydride MOD:00042
C, D	MSE	Parent Component: MET RESID: AA0033

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.