PDBsum entry 3b3b

Hydrolase

PDB id: 3b3b

Contents

Protein chain

866 a.a. *

Ligands

TRP

MLI

GOL ×3

Metals

_ZN

_NA ×2

Waters ×1004

* Residue conservation analysis

PDB id:

3b3b

Name:

Hydrolase

Title:

Crystal structure of e. Coli aminopeptidase n in complex with tryptophan

Structure:

Aminopeptidase n. Chain: a. Synonym: alpha-aminoacylpeptide hydrolase. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: aminopeptidase n. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.85Å R-factor: 0.153 R-free: 0.178

Authors:

A.Addlagatta

Key ref:

A.Addlagatta et al. (2008). Structural basis for the unusual specificity of Escherichia coli aminopeptidase N. Biochemistry, 47, 5303-5311. PubMed id: 18416562

Date:

19-Oct-07 Release date: 06-May-08

Protein chain

P04825  (AMPN_ECOLI) -  Aminopeptidase N from Escherichia coli (strain K12)

Seq: 870 a.a.

Struc: 866 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.11.2 - membrane alanyl aminopeptidase.
• Reaction: Release of an N-terminal amino acid, Xaa-|-Xbb- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.
• Cofactor: Zn(2+)

Biochemistry 47:5303-5311 (2008)

PubMed id: 18416562

Structural basis for the unusual specificity of Escherichia coli aminopeptidase N.

A.Addlagatta, L.Gay, B.W.Matthews.

ABSTRACT

Aminopeptidase N from Escherichia coli is a M1 class aminopeptidase with the active-site region related to that of thermolysin. The enzyme has unusual specificity, cleaving adjacent to the large, nonpolar amino acids Phe and Tyr but also cleaving next to the polar residues Lys and Arg. To try to understand the structural basis for this pattern of hydrolysis, the structure of the enzyme was determined in complex with the amino acids L-arginine, L-lysine, L-phenylalanine, L-tryptophan, and L-tyrosine. These amino acids all bind with their backbone atoms close to the active-site zinc ion and their side chain occupying the S1 subsite. This subsite is in the form of a cylinder, about 10 A in cross-section and 12 A in length. The bottom of the cylinder includes the zinc ion and a number of polar side chains that make multiple hydrogen-bonding and other interactions with the alpha-amino group and the alpha-carboxylate of the bound amino acid. The walls of the S1 cylinder are hydrophobic and accommodate the nonpolar or largely nonpolar side chains of Phe and Tyr. The top of the cylinder is polar in character and includes bound water molecules. The epsilon-amino group of the bound lysine side chain and the guanidinium group of arginine both make multiple hydrogen bonds to this part of the S1 site. At the same time, the hydrocarbon part of the lysine and arginine side chains is accommodated within the nonpolar walls of the S1 cylinder. This combination of hydrophobic and hydrophilic binding surfaces explains the ability of ePepN to cleave Lys, Arg, Phe, and Tyr. Another favored substrate has Ala at the P1 position. The short, nonpolar side chain of this residue can clearly be bound within the hydrophobic part of the S1 cylinder, but the reason for its facile hydrolysis remains uncertain.