A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi

TY - JOUR

T1 - A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi

AU - Bompard-Gilles, C

AU - Villeret, V

AU - Davies, G J

AU - Fanuel, L

AU - Joris, B

AU - Frere, J M

AU - Van Beeumen, J

PY - 2000/2/15

Y1 - 2000/2/15

N2 - Background: The L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. The DmpA active form is an alpha beta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide.Results: The crystal structure of the enzyme has been determined to 1.82 Angstrom resolution using the multiple isomorphous replacement method. The heterodimer folds into a single domain organised as an alpha beta beta alpha sandwich in which two mixed beta sheets are flanked on both sides by two a helices;Conclusions: DmpA shows no similarity to other known aminopeptidases in either fold or catalytic mechanism, and thus represents the first example of a novel family of aminopeptidases. The protein fold of DmpA does, however, show structural homology to members of the N-terminal nucleophile (Ntn) hydrolase superfamily. DmpA presents functionally equivalent residues in:the catalytic centre when compared with other Ntn hydrolases, and is therefore likely to use the same catalytic mechanism. In spite of this homology, the direction and connectivity of the secondary structure elements differ significantly from the consensus Ntn hydrolase topology. The DmpA structure thus characterises a new subfamily, but supports the common catalytic mechanism for these enzymes suggesting an evolutionary relationship.

AB - Background: The L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. The DmpA active form is an alpha beta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide.Results: The crystal structure of the enzyme has been determined to 1.82 Angstrom resolution using the multiple isomorphous replacement method. The heterodimer folds into a single domain organised as an alpha beta beta alpha sandwich in which two mixed beta sheets are flanked on both sides by two a helices;Conclusions: DmpA shows no similarity to other known aminopeptidases in either fold or catalytic mechanism, and thus represents the first example of a novel family of aminopeptidases. The protein fold of DmpA does, however, show structural homology to members of the N-terminal nucleophile (Ntn) hydrolase superfamily. DmpA presents functionally equivalent residues in:the catalytic centre when compared with other Ntn hydrolases, and is therefore likely to use the same catalytic mechanism. In spite of this homology, the direction and connectivity of the secondary structure elements differ significantly from the consensus Ntn hydrolase topology. The DmpA structure thus characterises a new subfamily, but supports the common catalytic mechanism for these enzymes suggesting an evolutionary relationship.

KW - autocatalysis

KW - crystal structure

KW - Ntn amidohydrolase

KW - serine aminopeptidase

KW - stereospecificity

KW - LENS LEUCINE AMINOPEPTIDASE

KW - HUMAN LYSOSOMAL ASPARTYLGLUCOSAMINIDASE

KW - TRANSITION-STATE ANALOG

KW - METHIONINE AMINOPEPTIDASE

KW - ANGSTROM RESOLUTION

KW - ESCHERICHIA-COLI

KW - 20S PROTEASOME

KW - MECHANISM

KW - ENZYME

KW - SITE

M3 - Article

SN - 0969-2126

VL - 8

SP - 153

EP - 162

JO - Structure

JF - Structure

IS - 2

ER -