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The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica

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Abstract

The aminopeptidase from Aeromonas proteolytica (AAP) contains two zinc ions in the active site and catalyzes the degradation of peptides. Herein we report the crystal structures of AAP at 0.95-Å resolution at neutral pH and at 1.24-Å resolution at low pH. The combination of these structures allowed the precise modeling of atomic positions, the identification of the metal bridging oxygen species, and insight into the physical properties of the metal ions. On the basis of these structures, a new putative catalytic mechanism is proposed for AAP that is likely relevant to all binuclear metalloproteases.

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Abbreviations

AAP:

Aminopeptidase from Aeromonas proteolytica

BuBA:

1-Butaneboronic acid

CSD:

Cambridge Structural Database

ESD:

Estimated standard deviation

HEPES:

4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid

LPA:

l-Leucinephosphonic acid

rms:

Root mean square

Tris:

Tris(hydroxymethyl)aminomethane

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Acknowledgements

This work was supported by the National Science Foundation (CHE-0549221 to R.C.H.), by the National Institutes of Health (GM26788 to G.A.P. and D.R.), and, in part, by the Macromolecular Training Grant from the National Institutes of Health (W.D.).

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Authors and Affiliations

  1. Program in Biophysics and Structural Biology, Brandeis University, 415 South Street, Waltham, MA, 02254-9110, USA

    William Desmarais

  2. The Rosenstiel Basic Medical Sciences Research Center, MS029, Brandeis University, 415 South Street, Waltham, MA, 02454-9110, USA

    William Desmarais, Gregory A. Petsko & Dagmar Ringe

  3. Department of Chemistry, Brandeis University, Waltham, MA, 02254-9110, USA

    Gregory A. Petsko & Dagmar Ringe

  4. Department of Biochemistry, Brandeis University, Waltham, MA, 02254-9110, USA

    Gregory A. Petsko & Dagmar Ringe

  5. Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322-0300, USA

    David L. Bienvenue, Krzysztof P. Bzymek & Richard C. Holz

Authors
  1. William Desmarais
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  2. David L. Bienvenue
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  3. Krzysztof P. Bzymek
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  4. Gregory A. Petsko
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  5. Dagmar Ringe
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  6. Richard C. Holz
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Corresponding authors

Correspondence to Gregory A. Petsko, Dagmar Ringe or Richard C. Holz.

Additional information

The coordinates for the 0.95-Å resolution structure and the 1.24-Å structure at pH 4.7 were deposited in the RCSB Protein Data Bank and have PDB ID numbers of 1RTQ and 2DEA, respectively.

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Desmarais, W., Bienvenue, D.L., Bzymek, K.P. et al. The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica . J Biol Inorg Chem 11, 398–408 (2006). https://doi.org/10.1007/s00775-006-0093-x

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  • DOI: https://doi.org/10.1007/s00775-006-0093-x

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