PDBsum entry 1q7l

Hydrolase

PDB id: 1q7l

Contents

Protein chains

192 a.a. *

88 a.a. *

Ligands

GLY ×2

Metals

_ZN ×4

Waters ×667

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Essential roles of zinc ligation and enzyme dimerization for catalysis in the aminoacylase-1/m20 family.

Authors

H.A.Lindner, V.V.Lunin, A.Alary, R.Hecker, M.Cygler, R.Ménard.

Ref.

J Biol Chem, 2003, 278, 44496-44504. [DOI no: 10.1074/jbc.M304233200]

PubMed id

12933810

Abstract

Members of the aminoacylase-1 (Acy1)/M20 family of aminoacylases and exopeptidases exist as either monomers or homodimers. They contain a zinc-binding domain and a second domain mediating dimerization in the latter case. The roles that both domains play in catalysis have been investigated for human Acy1 (hAcy1) by x-ray crystallography and by site-directed mutagenesis. Structure comparison of the dinuclear zinc center in a mutant of hAcy1 reported here with dizinc centers in related enzymes points to a difference in zinc ligation in the Acy1/M20 family. Mutational analysis supports catalytic roles of zinc ions, a vicinal glutamate, and a histidine from the dimerization domain. By complementing different active site mutants of hAcy1, we show that catalysis occurs at the dimer interface. Reinterpretation of the structure of a monomeric homolog, peptidase V, reveals that a domain insertion mimics dimerization. We conclude that monomeric and dimeric Acy1/M20 family members share a unique active site architecture involving both enzyme domains. The study may provide means to improve homologous carboxypeptidase G2 toward application in antibody-directed enzyme prodrug therapy.

Figure 1.
FIG. 1. Ribbon diagram of the zinc-binding domain in the T347G mutant of hAcy1. Glycine was modeled in place of a putative L-norleucine ligand molecule and is shown in a ball-and-stick representation. Zinc ions are represented as gray spheres.

Figure 3.
FIG. 3. Structures of the small domains of enzymes from the Acy1/M20 family. A, topology diagram for the lid domain in L. delbrueckii PepV and the dimerization domains from both monomers in Pseudomonas sp. CPG2. Subdomains 1 (gray) and 2 (white) of PepV show apparent similarity. However, strands 8 and 12 are only found in subdomain 1, and strands 3 and 7 are only found in subdomain 2. The -sheet composed of the latter two strands is also present in the dimerization domain of CPG2. B, backbone trace superposition of subdomains 1 and 2 in the lid domain of PepV (blue) and the two associated dimerization domains in CPG2 (red and green). Known active site residues in PepV are shown in a stick representation, from left to right, Arg350, Asn217 (both carboxyl-terminal docking), and His269 (transition state stabilization). Corresponding residues from CPG2 are also shown. The enlargement above additionally shows the corresponding residues in PepT. Arg288 from CPG2 (red) and Arg280 from PepT (yellow) reside in the monomer, which superimposes with subdomain 1 of PepV. Asn275 and His229 from CPG2 (green) and His223 in PepT (purple) are recruited from the opposite monomer which superimposes with subdomain 2 of PepV. In the structure of CPG2, the side chain of His229 shows a [1] rotation by about 90° relative to the other two structures and coordinates an additional interdimeric zinc ion in the protein crystal (not shown). C, multiple sequence alignment of the small domains in the PepV enzymes from L. delbrueckii (PEPV_LACDL) and Lactococcus lactis subsp. cremoris MG1363 (PEPV_LACLC) and from CPG2 (CBPG_PSES6), PepT (PEPT_SALTY), and hAcy1 (ACY1_HUMAN). Subdomain 1 and 2 in the lid domain of PepV are abbreviated sd1 and sd2, respectively. The alignment was assembled using an available alignment of the two PepV enzymes (15) and structure-based alignments of CPG2 to sd1 in L. Delbrueckii (29) and CPG2 to PepT (24). The sequences of the dimerization domain in hAcy1 and CPG2 were aligned manually. Strands (s) and helices (h), as identified in the crystal structures of PepV, CPG2, and PepT, are printed in red and blue, respectively. Their numbering in sd1 and sd2 of L. delbrueckii PepV is indicated in the corresponding colors above the aligned sequences. Residues that interact with the bound transition state analog Asp [PO[2]CH[2]]AlaOH in the PepV structure are in yellow boxes. Greek letters indicate the sites of rearrangement generated by the insertion of sd2 in the sequence of sd1 and their sequel.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 44496-44504) copyright 2003.