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Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member.

Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O
J Mol Biol 386 486-503 (2009)
Cited: 10 times
EuropePMC logo PMID: 19133276

Abstract

The Aspergillus niger genome contains four genes that encode proteins exhibiting greater than 30% amino acid sequence identity to the confirmed oxaloacetate acetyl hydrolase (OAH), an enzyme that belongs to the phosphoenolpyruvate mutase/isocitrate lyase superfamily. Previous studies have shown that a mutant A. niger strain lacking the OAH gene does not produce oxalate. To identify the function of the protein sharing the highest amino acid sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887, 57% identity), we produced the protein in Escherichia coli and purified it for structural and functional studies. A focused substrate screen was used to determine the catalytic function of An07g08390 as (2R,3S)-dimethylmalate lyase (DMML): k(cat)=19.2 s(-1) and K(m)=220 microM. DMML also possesses significant OAH activity (k(cat)=0.5 s(-1) and K(m) =220 microM). DNA array analysis showed that unlike the A. niger oah gene, the DMML encoding gene is subject to catabolite repression. DMML is a key enzyme in bacterial nicotinate catabolism, catalyzing the last of nine enzymatic steps. This pathway does not have a known fungal counterpart. BLAST analysis of the A. niger genome for the presence of a similar pathway revealed the presence of homologs to only some of the pathway enzymes. This and the finding that A. niger does not thrive on nicotinamide as a sole carbon source suggest that the fungal DMML functions in a presently unknown metabolic pathway. The crystal structure of A. niger DMML (in complex with Mg(2+) and in complex with Mg(2+) and a substrate analog: the gem-diol of 3,3-difluoro-oxaloacetate) was determined for the purpose of identifying structural determinants of substrate recognition and catalysis. Structure-guided site-directed mutants were prepared and evaluated to test the contributions made by key active-site residues. In this article, we report the results in the broader context of the lyase branch of the phosphoenolpyruvate mutase/isocitrate lyase superfamily to provide insight into the evolution of functional diversity.

Articles - 3fa3 mentioned but not cited (1)

  1. Structure of oxalacetate acetylhydrolase, a virulence factor of the chestnut blight fungus. Chen C, Sun Q, Narayanan B, Nuss DL, Herzberg O. J Biol Chem 285 26685-26696 (2010)


Articles citing this publication (9)

  1. 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities. Kuipers RK, Joosten HJ, van Berkel WJ, Leferink NG, Rooijen E, Ittmann E, van Zimmeren F, Jochens H, Bornscheuer U, Vriend G, dos Santos VA, Schaap PJ. Proteins 78 2101-2113 (2010)
  2. Correlated mutation analyses on super-family alignments reveal functionally important residues. Kuipers RK, Joosten HJ, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NG, van Berkel WJ, Vriend G, Schaap PJ. Proteins 76 608-616 (2009)
  3. The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR, Tsang A, de Vries RP. Stud Mycol 91 61-78 (2018)
  4. Novel tools for extraction and validation of disease-related mutations applied to Fabry disease. Kuipers R, van den Bergh T, Joosten HJ, Lekanne dit Deprez RH, Mannens MM, Schaap PJ. Hum Mutat 31 1026-1032 (2010)
  5. Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase. Ibeji CU, Salleh NAM, Sum JS, Ch'ng ACW, Lim TS, Choong YS. Sci Rep 10 18925 (2020)
  6. Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. Schürmann M, Demming RM, Krewing M, Rose J, Wübbeler JH, Steinbüchel A. J Bacteriol 196 882-893 (2014)
  7. QM/MM investigation of the reaction rates of substrates of 2,3-dimethylmalate lyase: A catabolic protein isolated from Aspergillus niger. Chotpatiwetchkul W, Jongkon N, Hannongbua S, Gleeson MP. J Mol Graph Model 68 29-38 (2016)
  8. Residues Asn214, Gln211, Glu219 and Gln221 contained in the subfamily 3 catalytic signature of the isocitrate lyase from Pseudomonas aeruginosa are involved in its catalytic and thermal properties. Campos-Garcia J, Diaz-Perez C, Diaz-Perez AL. World J Microbiol Biotechnol 29 991-999 (2013)
  9. Regulatory-systemic approach in Aspergillus niger for bioleaching improvement by controlling precipitation. Naderi A, Vakilchap F, Motamedian E, Mousavi SM. Appl Microbiol Biotechnol 107 7331-7346 (2023)


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