Functional annotation and structural characterization of a novel lactonase hydrolyzing d-xylono-1,4-lactone-5-phosphate and l -arabino-1,4-lactone-5- phosphate

Magdalena Korczynska, Dao Feng Xiang, Zhening Zhang, Chengfu Xu, Tamari Narindoshvili, Siddhesh S. Kamat, Howard J. Williams, Shawn S. Chang, Peter Kolb, Brandan Hillerich, J. Michael Sauder, Stephen K. Burley, Steven C. Almo, Subramanyam Swaminathan, Brian K. Shoichet, Frank M. Raushel

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

A novel lactonase from Mycoplasma synoviae 53 (MS53-0025) and Mycoplasma agalactiae PG2 (MAG-6390) was characterized by protein structure determination, molecular docking, gene context analysis, and library screening. The crystal structure of MS53-0025 was determined to a resolution of 2.06 Å. This protein adopts a typical amidohydrolase (β/α)8-fold and contains a binuclear zinc center located at the C-terminal end of the β-barrel. A phosphate molecule was bound in the active site and hydrogen bonds to Lys217, Lys244, Tyr245, Arg275, and Tyr278. Both docking and gene context analysis were used to narrow the theoretical substrate profile of the enzyme, thus directing empirical screening to identify that MS53-0025 and MAG-6390 catalyze the hydrolysis of d-xylono-1,4-lactone-5-phosphate (2) with kcat/Km values of 4.7 × 104 and 5.7 × 104 M-1 s-1 and l-arabino-1,4-lactone- 5-phosphate (7) with kcat/Km values of 1.3 × 10 4 and 2.2 × 104 M-1 s-1, respectively. The identification of the substrate profile of these two phospho-furanose lactonases emerged only when all methods were integrated and therefore provides a blueprint for future substrate identification of highly related amidohydrolase superfamily members.

Original languageEnglish (US)
Pages (from-to)4727-4738
Number of pages12
JournalBiochemistry
Volume53
Issue number28
DOIs
StatePublished - Jul 22 2014

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Lactones
Amidohydrolases
Phosphates
Mycoplasma agalactiae
Screening
Mycoplasma synoviae
Substrates
Genes
Blueprints
Molecular Structure
Zinc
Hydrogen
Hydrolysis
Catalytic Domain
Hydrogen bonds
Proteins
Crystal structure
Molecules
Enzymes

ASJC Scopus subject areas

  • Biochemistry

Cite this

Functional annotation and structural characterization of a novel lactonase hydrolyzing d-xylono-1,4-lactone-5-phosphate and l -arabino-1,4-lactone-5- phosphate. / Korczynska, Magdalena; Xiang, Dao Feng; Zhang, Zhening; Xu, Chengfu; Narindoshvili, Tamari; Kamat, Siddhesh S.; Williams, Howard J.; Chang, Shawn S.; Kolb, Peter; Hillerich, Brandan; Sauder, J. Michael; Burley, Stephen K.; Almo, Steven C.; Swaminathan, Subramanyam; Shoichet, Brian K.; Raushel, Frank M.

In: Biochemistry, Vol. 53, No. 28, 22.07.2014, p. 4727-4738.

Research output: Contribution to journalArticle

Korczynska, M, Xiang, DF, Zhang, Z, Xu, C, Narindoshvili, T, Kamat, SS, Williams, HJ, Chang, SS, Kolb, P, Hillerich, B, Sauder, JM, Burley, SK, Almo, SC, Swaminathan, S, Shoichet, BK & Raushel, FM 2014, 'Functional annotation and structural characterization of a novel lactonase hydrolyzing d-xylono-1,4-lactone-5-phosphate and l -arabino-1,4-lactone-5- phosphate', Biochemistry, vol. 53, no. 28, pp. 4727-4738. https://doi.org/10.1021/bi500595c
Korczynska, Magdalena ; Xiang, Dao Feng ; Zhang, Zhening ; Xu, Chengfu ; Narindoshvili, Tamari ; Kamat, Siddhesh S. ; Williams, Howard J. ; Chang, Shawn S. ; Kolb, Peter ; Hillerich, Brandan ; Sauder, J. Michael ; Burley, Stephen K. ; Almo, Steven C. ; Swaminathan, Subramanyam ; Shoichet, Brian K. ; Raushel, Frank M. / Functional annotation and structural characterization of a novel lactonase hydrolyzing d-xylono-1,4-lactone-5-phosphate and l -arabino-1,4-lactone-5- phosphate. In: Biochemistry. 2014 ; Vol. 53, No. 28. pp. 4727-4738.
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abstract = "A novel lactonase from Mycoplasma synoviae 53 (MS53-0025) and Mycoplasma agalactiae PG2 (MAG-6390) was characterized by protein structure determination, molecular docking, gene context analysis, and library screening. The crystal structure of MS53-0025 was determined to a resolution of 2.06 {\AA}. This protein adopts a typical amidohydrolase (β/α)8-fold and contains a binuclear zinc center located at the C-terminal end of the β-barrel. A phosphate molecule was bound in the active site and hydrogen bonds to Lys217, Lys244, Tyr245, Arg275, and Tyr278. Both docking and gene context analysis were used to narrow the theoretical substrate profile of the enzyme, thus directing empirical screening to identify that MS53-0025 and MAG-6390 catalyze the hydrolysis of d-xylono-1,4-lactone-5-phosphate (2) with kcat/Km values of 4.7 × 104 and 5.7 × 104 M-1 s-1 and l-arabino-1,4-lactone- 5-phosphate (7) with kcat/Km values of 1.3 × 10 4 and 2.2 × 104 M-1 s-1, respectively. The identification of the substrate profile of these two phospho-furanose lactonases emerged only when all methods were integrated and therefore provides a blueprint for future substrate identification of highly related amidohydrolase superfamily members.",
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AU - Korczynska, Magdalena

AU - Xiang, Dao Feng

AU - Zhang, Zhening

AU - Xu, Chengfu

AU - Narindoshvili, Tamari

AU - Kamat, Siddhesh S.

AU - Williams, Howard J.

AU - Chang, Shawn S.

AU - Kolb, Peter

AU - Hillerich, Brandan

AU - Sauder, J. Michael

AU - Burley, Stephen K.

AU - Almo, Steven C.

AU - Swaminathan, Subramanyam

AU - Shoichet, Brian K.

AU - Raushel, Frank M.

PY - 2014/7/22

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N2 - A novel lactonase from Mycoplasma synoviae 53 (MS53-0025) and Mycoplasma agalactiae PG2 (MAG-6390) was characterized by protein structure determination, molecular docking, gene context analysis, and library screening. The crystal structure of MS53-0025 was determined to a resolution of 2.06 Å. This protein adopts a typical amidohydrolase (β/α)8-fold and contains a binuclear zinc center located at the C-terminal end of the β-barrel. A phosphate molecule was bound in the active site and hydrogen bonds to Lys217, Lys244, Tyr245, Arg275, and Tyr278. Both docking and gene context analysis were used to narrow the theoretical substrate profile of the enzyme, thus directing empirical screening to identify that MS53-0025 and MAG-6390 catalyze the hydrolysis of d-xylono-1,4-lactone-5-phosphate (2) with kcat/Km values of 4.7 × 104 and 5.7 × 104 M-1 s-1 and l-arabino-1,4-lactone- 5-phosphate (7) with kcat/Km values of 1.3 × 10 4 and 2.2 × 104 M-1 s-1, respectively. The identification of the substrate profile of these two phospho-furanose lactonases emerged only when all methods were integrated and therefore provides a blueprint for future substrate identification of highly related amidohydrolase superfamily members.

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