Crystal Structures of Staphylococcus aureus Methionine Aminopeptidase Complexed with Keto Heterocycle and Aminoketone Inhibitors Reveal the Formation of a Tetrahedral Intermediate

Douangamath, A.; Dale, Glenn E.; D’Arcy, Allan; Almstetter, Michael; Eckl, Robert; Frutos-Hoener, Annabelle; Henkel, Bernd; Illgen, Katrin; Nerdinger, Sven; Schulz, Henk; Macsweeney, Aengus; Thormann, Michael; Treml, Andreas; Pierau, Sabine; Wadman, Sjoerd; Oefner, Christian

doi:10.1021/jm034188j

Cited by 47 publications

(36 citation statements)

References 36 publications

(85 reference statements)

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“…Undoubtedly, Co(II) is an excellent activator of purified MetAP apoenzyme, and the Co(II)-form MetAP is responsible for the discovery of most of the current MetAP inhibitors (22,23,(42)(43)(44) and has provided structural and mechanistic insight of the catalysis and inhibition of this therapeutically important family of enzymes (14). However, most Co(II) proteins are vitamin B12-dependent enzymes, and MetAP is among the limited number of enzymes that have Co(II) in a non-B12 form (45).…”

Section: Discussionmentioning

confidence: 99%

FE(II) Is the Native Cofactor for Escherichia coli Methionine Aminopeptidase

Chai

Wang

2008

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 99%

FE(II) Is the Native Cofactor for Escherichia coli Methionine Aminopeptidase

Chai

Wang

2008

Journal of Biological Chemistry

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“…[10] Affinity towards MetAP auxiliary cobalt ion is complexed in a nearly perfect octahedral geometry by two nitrogen atoms of thiabendazole, one histidine nitrogen atom (His 79), and three water molecules. Additionally, we determined the 3D structure of E. coli MetAP in complex with the lead compound 2, which has been previously identified by Luo et al [3] to a resolution of 1.6 .…”

Section: Structure Of Metap Complexmentioning

confidence: 99%

Metal Ions as Cofactors for the Binding of Inhibitors to Methionine Aminopeptidase: A Critical View of the Relevance of In Vitro Metalloenzyme Assays

Schiffmann

Heine²,

Klebe³

et al. 2005

Angew Chem Int Ed

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Thiabendazole is a potent inhibitor of E. coli methionine aminopeptidase (MetAP) in vitro. Crystallographic structures of MetAP complexed with this and two other inhibitors show that binding is mediated by an auxiliary metal ion (see picture). This effect results from the high concentration of metal ions under in vitro conditions, and should be taken into account in assays for inhibitors of metal‐dependent enzymes.

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“…These metal ions are suggested to bind and activate the water for deprotonation and assist the nucleophilic attack, whereas the metal ion M2 also binds the free unprotonated amino group of the methionine residue (P1) of the substrate for a productive bound conformation. In some recent structures, a third divalent metal ion is also present, serving as a bridge between a small molecule ligand and active-site groups on the enzyme (11,(22)(23)(24). Despite the great number of x-ray structures of these enzymes that show two or even three divalent metal ions bound in the active-site region, metal titration studies indicate that some of these metalloaminopeptidases can function fully with only a single metal ion bound.…”

mentioning

confidence: 99%

Structural basis of catalysis by monometalated methionine aminopeptidase

Xie

Qiang

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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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.metalloprotease ͉ protein structure ͉ enzyme inhibition ͉ drug discovery ͉ metal occupancy A ll newly synthesized proteins have an amino-terminal methionine residue corresponding to the start codon AUG. In a significant number of cases, this initiating methionine residue is removed, either co-or posttranslationally, by the enzyme methionine aminopeptidase (MetAP) (1). In bacteria, this enzyme is the product of a single gene, and it is absolutely essential for bacterial survival, as demonstrated by gene deletion experiments in Escherichia coli (2) and Salmonella typhimurium (3). The single but critically essential MetAP enzyme of bacteria thus stands out as an attractive target for the design of antibacterial agents (4). Eukaryotes, on the other hand, have two distinct MetAPs, types I and II, arising from different genes (5). The human type II MetAP is a target of the antiangiogenic compounds fumagillin, ovalicin, and TNP-470 (6-8). Bengamides inhibit both types of MetAP (9) and cause inhibition of the growth of several human tumor cell lines in vitro at low-nanomolar concentrations. Therefore, human MetAPs may also serve as targets for the development of new anticancer agents. Some small molecules that inhibit MetAPs potently in vitro are known, but they lack potent antibacterial (10-12) or antiangiogenic (13) activities. One reason for this failure may be that they do not penetrate the bacterial or mammalian cells to...

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Crystal Structures of Staphylococcus aureus Methionine Aminopeptidase Complexed with Keto Heterocycle and Aminoketone Inhibitors Reveal the Formation of a Tetrahedral Intermediate

Cited by 47 publications

References 36 publications

FE(II) Is the Native Cofactor for Escherichia coli Methionine Aminopeptidase

FE(II) Is the Native Cofactor for Escherichia coli Methionine Aminopeptidase

Metal Ions as Cofactors for the Binding of Inhibitors to Methionine Aminopeptidase: A Critical View of the Relevance of In Vitro Metalloenzyme Assays

Structural basis of catalysis by monometalated methionine aminopeptidase

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