6D6Z

Structure of the malate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum

Summary for 6D6Z

• Entry DOI: 10.2210/pdb6d6z/pdb
• Descriptor: Malate racemase Mar2 (2 entities in total)
• Functional Keywords: lar, lactate racemase, isomerase
• Biological source: Thermoanaerobacterium thermosaccharolyticum (strain ATCC 7956 / DSM 571 / NCIB 9385 / NCA 3814) (Clostridium thermosaccharolyticum)
• Total number of polymer chains: 1
• Total formula weight: 47559.42

Authors

Fellner, M.,Hausinger, R.P.,Hu, J. (deposition date: 2018-04-23, release date: 2019-04-24, Last modification date: 2023-10-04)

Primary citation

Desguin, B.,Urdiain-Arraiza, J.,Da Costa, M.,Fellner, M.,Hu, J.,Hausinger, R.P.,Desmet, T.,Hols, P.,Soumillion, P.
Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases.
Sci Rep, 10:18123-18123, 2020

PubMed Abstract: Isomerization reactions are fundamental in biology. Lactate racemase, which isomerizes L- and D-lactate, is composed of the LarA protein and a nickel-containing cofactor, the nickel-pincer nucleotide (NPN). In this study, we show that LarA is part of a superfamily containing many different enzymes. We overexpressed and purified 13 lactate racemase homologs, incorporated the NPN cofactor, and assayed the isomerization of different substrates guided by gene context analysis. We discovered two malate racemases, one phenyllactate racemase, one α-hydroxyglutarate racemase, two D-gluconate 2-epimerases, and one short-chain aliphatic α-hydroxyacid racemase among the tested enzymes. We solved the structure of a malate racemase apoprotein and used it, along with the previously described structures of lactate racemase holoprotein and D-gluconate epimerase apoprotein, to identify key residues involved in substrate binding. This study demonstrates that the NPN cofactor is used by a diverse superfamily of α-hydroxyacid racemases and epimerases, widely expanding the scope of NPN-dependent enzymes.

PubMed: 33093595
DOI: 10.1038/s41598-020-74802-6

Experimental method

X-RAY DIFFRACTION (2.38 Å)