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Crystal structure of the S187F variant of human liver alanine: Aminotransferase associated with primary hyperoxaluria type I and its functional implications

Authors

  • Elisa Oppici,

    1. Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Verona, Italy
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    • Elisa Oppici and Krisztian Fodor contributed equally to this work.

  • Krisztian Fodor,

    1. EMBL c/o DESY, Hamburg, Germany
    Current affiliation:
    1. Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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    • Elisa Oppici and Krisztian Fodor contributed equally to this work.

  • Alessandro Paiardini,

    1. Department of Biochemical Sciences “A. Rossi Fanelli”, University “La Sapienza”, Roma, Italy
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    • Alessandro Paiardini and Chris Williams contributed equally to this work.Krisztian Fodor's current address is Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/C, Budapest, Hungary.

  • Chris Williams,

    1. EMBL c/o DESY, Hamburg, Germany
    Current affiliation:
    1. Molecular Cell Biology, University of Groningen, The Netherlands
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    • Alessandro Paiardini and Chris Williams contributed equally to this work.Krisztian Fodor's current address is Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/C, Budapest, Hungary.

  • Carla Borri Voltattorni,

    1. Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Verona, Italy
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  • Matthias Wilmanns,

    1. EMBL c/o DESY, Hamburg, Germany
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  • Barbara Cellini

    Corresponding author
    • Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Verona, Italy
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Errata

This article is corrected by:

  1. Errata: Crystal structure of the S187F variant of human liver alanine: Aminotransferase associated with primary hyperoxaluria type I and its functional implications Volume 82, Issue 1, 171, Article first published online: 11 December 2013

  • Chris Williams's current address is Molecular Cell Biology, University of Groningen, The Netherlands.

Correspondence to: Barbara Cellini, Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Strada Le Grazie 8 37134 Verona, Italy. E-mail: barbara.cellini@univr.it

ABSTRACT

The substitution of Ser187, a residue located far from the active site of human liver peroxisomal alanine:glyoxylate aminotransferase (AGT), by Phe gives rise to a variant associated with primary hyperoxaluria type I. Unexpectedly, previous studies revealed that the recombinant form of S187F exhibits a remarkable loss of catalytic activity, an increased pyridoxal 5′-phosphate (PLP) binding affinity and a different coenzyme binding mode compared with normal AGT. To shed light on the structural elements responsible for these defects, we solved the crystal structure of the variant to a resolution of 2.9 Å. Although the overall conformation of the variant is similar to that of normal AGT, we noticed: (i) a displacement of the PLP-binding Lys209 and Val185, located on the re and si side of PLP, respectively, and (ii) slight conformational changes of other active site residues, in particular Trp108, the base stacking residue with the pyridine cofactor moiety. This active site perturbation results in a mispositioning of the AGT-pyridoxamine 5′-phosphate (PMP) complex and of the external aldimine, as predicted by molecular modeling studies. Taken together, both predicted and observed movements caused by the S187F mutation are consistent with the following functional properties of the variant: (i) a 300- to 500-fold decrease in both the rate constant of L-alanine half-transamination and the kcat of the overall transamination, (ii) a different PMP binding mode and affinity, and (iii) a different microenvironment of the external aldimine. Proposals for the treatment of patients bearing S187F mutation are discussed on the basis of these results. Proteins 2013; 81:1457–1465. © 2013 Wiley Periodicals, Inc.

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