7S91

Structure of the malate racemase mar2 apoprotein from Thermoanaerobacterium thermosaccharolyticum at 2.25 angstroms resolution

Summary for 7S91

• Entry DOI: 10.2210/pdb7s91/pdb
• Descriptor: Malate racemase Mar2, CHLORIDE ION (3 entities in total)
• Functional Keywords: catalytic activity, isomerase activity, racemase and epimerase activity racemase acting on hydroxy acids and derivatives, isomerase
• Biological source: Thermoanaerobacterium thermosaccharolyticum (strain ATCC 7956 / DSM 571 / NCIB 9385 / NCA 3814)
• Total number of polymer chains: 1
• Total formula weight: 47630.32

Authors

Gatreddi, S.,Hausinger, R.P.,Hu, J. (deposition date: 2021-09-20, release date: 2021-10-13, Last modification date: 2023-10-25)

Primary citation

Gatreddi, S.,Urdiain-Arraiza, J.,Desguin, B.,Hausinger, R.P.,Hu, J.
Structural and mutational characterization of a malate racemase from the LarA superfamily.
Biometals, 36:303-313, 2023

PubMed Abstract: The LarA superfamily consists of nickel-dependent enzymes catalyzing racemization/epimerization reactions using a variety of α-hydroxy acids. The first-characterized LarA, a lactate racemase from Lactobacillus plantarum, led to the discovery of the nickel-pincer nucleotide (NPN) cofactor that is utilized by family members with alternative substrates, including malate racemase from Thermoanaerobacterium thermosaccharolyticum (Mar2). In this work, a higher resolution crystal structure of Mar2 was obtained with better data quality that revealed new structural and dynamic characteristics of the protein. A model of the Mar2 structure with bound cofactor and substrate was generated to uncover the common and the unique features among two distinct subgroups in the LarA superfamily. In addition, structure-guided mutational studies were used to examine the importance of residues that are modeled to interact with NPN and to explore which residues were critical for conferring specificity for malate. In particular, substitution of two residues involved in substrate binding in Mar2 to match the corresponding residues in LarA led to the acquisition of low levels of lactate racemase activity. Of additional interest, the substrate spectrum was expanded to include tartrate, an analog of malate. These new findings will help to better understand structure-function relationships of many other LarA homologs that are broadly distributed in bacterial and archaeal species.

PubMed: 35182264
DOI: 10.1007/s10534-022-00372-x

Experimental method

X-RAY DIFFRACTION (2.25 Å)