PDBsum entry: 2gtx

Hydrolase

PDB id: 2gtx

Contents

Protein chains

261 a.a. *

Ligands

NLP ×2

Metals

_MN ×2

_NA ×2

Waters ×267

* Residue conservation analysis

PDB id:

2gtx

Name:

Hydrolase

Title:

Structural basis of catalysis by mononuclear methionine aminopeptidase

Structure:

Methionine aminopeptidase. Chain: a, b. Synonym: map, peptidase m. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: map. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.196 R-free: 0.241

Authors:

Q.Z Ye

Key ref:

Q.Z.Ye et al. (2006). Structural basis of catalysis by monometalated methionine aminopeptidase. Proc Natl Acad Sci U S A, 103, 9470-9475. PubMed id: 16769889 DOI: 10.1073/pnas.0602433103

Date:

28-Apr-06 Release date: 04-Jul-06

Protein chains

P0AE18  (AMPM_ECOLI) -  Methionine aminopeptidase

Seq: 264 a.a.

Struc: 261 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.11.18 - Methionyl aminopeptidase.
• Reaction: Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
• Cofactor: Cobalt

 Gene Ontology (GO) functional annotation 

• Biological process: cellular process (3 terms)
• Biochemical function: protein binding (8 terms)

DOI no: 10.1073/pnas.0602433103

Proc Natl Acad Sci U S A 103:9470-9475 (2006)

PubMed id: 16769889

Structural basis of catalysis by monometalated methionine aminopeptidase.

Q.Z.Ye, S.X.Xie, Z.Q.Ma, M.Huang, R.P.Hanzlik.

ABSTRACT

Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of Escherichia coli MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.

Selected figure(s)

Figure 3.
Fig. 3. Chemical and x-ray structures. (A) Chemical structures of L-methionine (Met), NleP, and the peptide inhibitor AHHpA-Ala-Leu-Val-Phe-OMe. (B) Stereoview of overlay of E. coli MetAP structures of the mono-Mn(II) form with NleP (red), the di-Mn(II) form with NleP (green), and the di-Co(II) form with AHHpA-Ala-Leu-Val-Phe-OMe (yellow; only the AHHpA-Ala-Leu moiety shown here was observed in the crystal structure).

Figure 4.
Fig. 4. Proposed models and catalytic mechanism. Proposed models of tripeptide substrate Met-Ala-Leu (A) and its tetrahedral intermediate (B) bound to the active site. A schematic drawing of the proposed catalytic mechanism of monometalated MetAP is shown in C.

Figures were selected by an automated process.