PDBsum entry 3b3v

Hydrolase

PDB id: 3b3v

Contents

Protein chain

291 a.a. *

Ligands

SCN ×2

VAL

Metals

_ZN ×2

_NA ×3

Waters ×218

* Residue conservation analysis

PDB id:

3b3v

Name:

Hydrolase

Title:

Crystal structure of the s228a mutant of the aminopeptidase from vibrio proteolyticus

Structure:

Bacterial leucyl aminopeptidase. Chain: a. Fragment: residues 107-397. Engineered: yes. Mutation: yes

Source:

Vibrio proteolyticus. Organism_taxid: 671. Strain: dsm 30189 / ifo 13287 / lmg 3772 / ncimb 1326. Atcc: 15338. Gene: aap. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.22Å R-factor: 0.150 R-free: 0.171

Authors:

N.J.Ataie,Q.Q.Hoang,M.P.D.Zahniser,A.Milne,G.A.Petsko,D.Ringe

Key ref:

N.J.Ataie et al. (2008). Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus. Biochemistry, 47, 7673-7683. PubMed id: 18576673

Date:

22-Oct-07 Release date: 27-Nov-07

Protein chain

Q01693  (AMPX_VIBPR) -  Bacterial leucyl aminopeptidase from Vibrio proteolyticus

Seq: 504 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.11.10 - bacterial leucyl aminopeptidase.
• Reaction: Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
• Cofactor: Zn(2+)

Biochemistry 47:7673-7683 (2008)

PubMed id: 18576673

Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus.

N.J.Ataie, Q.Q.Hoang, M.P.Zahniser, Y.Tu, A.Milne, G.A.Petsko, D.Ringe.

ABSTRACT

The chemical properties of zinc make it an ideal metal to study the role of coordination strain in enzymatic rate enhancement. The zinc ion and the protein residues that are bound directly to the zinc ion represent a functional charge/dipole complex, and polarization of this complex, which translates to coordination distortion, may tune electrophilicity, and hence, reactivity. Conserved protein residues outside of the charge/dipole complex, such as second-shell residues, may play a role in supporting the electronic strain produced as a consequence of functional polarization. To test the correlation between charge/dipole polarity and ligand binding affinity, structure-function studies were carried out on the dizinc aminopeptidase from Vibrio proteolyticus. Alanine substitutions of S228 and M180 resulted in catalytically diminished enzymes whose crystal structures show very little change in the positions of the metal ions and the protein residues. However, more detailed inspections of the crystal structures show small positional changes that account for differences in the zinc ion coordination geometry. Measurements of the binding affinity of leucine phosphonic acid, a transition state analogue, and leucine, a product, show a correlation between coordination geometry and ligand binding affinity. These results suggest that the coordination number and polarity may tune the electrophilicity of zinc. This may have provided the evolving enzyme with the ability to discriminate between reaction coordinate species.