PDBsum entry: 1jaw

Proline peptidase

PDB id: 1jaw

Contents

Protein chain

440 a.a. *

Ligands

ACT

Metals

_MN ×2

Waters ×262

* Residue conservation analysis

PDB id:

1jaw

Name:

Proline peptidase

Title:

Aminopeptidase p from e. Coli low ph form

Structure:

Aminopeptidase p. Chain: a. Synonym: ampp. Other_details: active site 2 manganese

Source:

Escherichia coli. Organism_taxid: 562. Strain: an1459/ppl670. Cellular_location: cytoplasm

Biol. unit:

Homo-Tetramer (from PDB file)

Resolution:

2.70Å R-factor: 0.182 R-free: 0.227

Authors:

M.C.J.Wilce,C.S.Bond,P.E.Lilley,N.E.Dixon,H.C.Freeman, J.M.Guss

Key ref:

M.C.Wilce et al. (1998). Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. Proc Natl Acad Sci U S A, 95, 3472-3477. PubMed id: 9520390 DOI: 10.1073/pnas.95.7.3472

Date:

22-Dec-97 Release date: 06-Apr-99

Protein chain

P15034  (AMPP_ECOLI) -  Xaa-Pro aminopeptidase

Seq: 441 a.a.

Struc: 440 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.11.9 - Xaa-Pro aminopeptidase.
• Reaction: Release of any N-terminal amino acid, including proline, that is linked with proline, even from a dipeptide or tripeptide.
• Cofactor: Manganese or cobalt

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: cellular process (2 terms)
• Biochemical function: protein binding (8 terms)

DOI no: 10.1073/pnas.95.7.3472

Proc Natl Acad Sci U S A 95:3472-3477 (1998)

PubMed id: 9520390

Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli.

M.C.Wilce, C.S.Bond, N.E.Dixon, H.C.Freeman, J.M.Guss, P.E.Lilley, J.A.Wilce.

ABSTRACT

The structure of the proline-specific aminopeptidase (EC 3.4.11.9) from Escherichia coli has been solved and refined for crystals of the native enzyme at a 2.0-A resolution, for a dipeptide-inhibited complex at 2.3-A resolution, and for a low-pH inactive form at 2.7-A resolution. The protein crystallizes as a tetramer, more correctly a dimer of dimers, at both high and low pH, consistent with observations from analytical ultracentrifuge studies that show that the protein is a tetramer under physiological conditions. The monomer folds into two domains. The active site, in the larger C-terminal domain, contains a dinuclear manganese center in which a bridging water molecule or hydroxide ion appears poised to act as the nucleophile in the attack on the scissile peptide bond of Xaa-Pro. The metal-binding residues are located in a single subunit, but the residues surrounding the active site are contributed by three subunits. The fold of the protein resembles that of creatine amidinohydrolase (creatinase, not a metalloenzyme). The C-terminal catalytic domain is also similar to the single-domain enzyme methionine aminopeptidase that has a dinuclear cobalt center.

Selected figure(s)

Figure 1.
Fig. 1. (a) Orthogonal views of the tetramer of AMPP. Chain A is cyan, chain B is blue, chain C is green, and chain D is red. Mn2+ ions in the dinuclear active site are enlarged magenta spheres. (b) Stereo C^ trace of AMPP. Residues are color ramped from blue at the N terminus to red at the C terminus.

Figure 2.
Fig. 2. (a) Stereo view of the catalytic site of AMPP for native crystals at pH 8.3. Residues are colored by atom type. (b) Stereo view of the catalytic site of AMPP for crystals at pH 8.3 showing omit difference electron density for the inhibitor Pro-Leu contoured at 4 . (c) Stereo view of the catalytic site of AMPP for crystals at pH 4.6 showing omit difference electron density for coordinated acetate ion contoured at 4 .

Figures were selected by the author.