6U7L

2.75 Angstrom Crystal Structure of Galactarate Dehydratase from Escherichia coli.

Summary for 6U7L

• Entry DOI: 10.2210/pdb6u7l/pdb
• Descriptor: Galactarate dehydratase (L-threo-forming), CALCIUM ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: structural genomics, center for structural genomics of infectious diseases, csgid, galactarate dehydratase, gard, lyase
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 4
• Total formula weight: 229754.56

Authors

Minasov, G.,Shuvalova, L.,Wawrzak, Z.,Dubrovska, I.,Kiryukhina, O.,Endres, M.,Satchell, K.J.F.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2019-09-03, release date: 2019-11-06, Last modification date: 2025-04-02)

Primary citation

Rosas-Lemus, M.,Minasov, G.,Shuvalova, L.,Wawrzak, Z.,Kiryukhina, O.,Mih, N.,Jaroszewski, L.,Palsson, B.,Godzik, A.,Satchell, K.J.F.
Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment.
Protein Sci., 29:711-722, 2020

PubMed Abstract: Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a β-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel β-sheet supported by nine α-helices. A metal binding site in the C-terminal domain is occupied by Ca . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes.

PubMed: 31811683
DOI: 10.1002/pro.3796

Experimental method

X-RAY DIFFRACTION (2.75 Å)