Human methionine aminopeptidase-2 (MetAP-2) is a bifunctional cytosolic protein that plays a critical role in the regulation of post-translational processing and protein synthesis. It is responsible for the hydrolysis of N-terminal methionine from the majority of newly synthesized proteins. It is a metalloprotease containing cobalt .
MetAP-2 is the molecular target for angiogenesis inhibitors. Angiogenesis is the growth of new blood vessels, which is the pathogenic determinant in tumor progression, diabetic retinopathy and rheumatoid arthritis. This protein was crystallized with and without the synthetic inhibitor analogue, fumagillin. Since fumagillin is known to inhibit cancer cell proliferation, it is implied that MetAP-2 plays a complex role in tumor progression. MetAP-2 is currently being researched as a possible drug target for cancer treatment.
The overall topology of MetAP-2 was defined by the early crystallographic studies of its cousin MetAP-1 from E. coli and MetAP-2 from P. furiosus. Human methionine aminopeptidase-2 contains a central beta sheet with the active site at the center of the sheet's concavity. The active site is a deep pocket that contains two cobalts at its base. The active site also contains a completely covered side pocket that is the specificity site for the N-terminal methionine side chain of natural substrates. There are several catalytic residues which include: Phe219, His231, Leu328, His331, Ile338, His339, Tyr444, and Leu447. His231 and Tyr444 are the most important residues.
The reaction mechanism for MetAP-2 is dependent on multiple reactions. When there is no substrate in the active pocket, to cobalts are coordinated by Asp251, Asp262, His331, Glu364, Glu459, and a water molecule. Asp262 and Glu459 coordinate with both Co2+ molecules. Asp251 only coordinates with cobalt 1 while Glu364, His331 and the water molecule only coordinate with cobalt 2. There is limited information of the actual catalytic mechanism of MetAP-2. However, it is understood how the catalytic mechanism is inhibited by inhibitors such as fumagillin. When the mimic substrate is present, it occupies the side pocket near the active site. It hydrophobically interacts with His331 at the mouth of the pocket along with Tyr444, Ile338, His339, and Phe219. The water molecule forms hydrogen bonds with the side chain epoxide and methoxyl group. The long unsaturated side chain protrudes from the binding pocket and makes two hydrophobic contacts with Leu328 and Leu447. The terminal carboxyl of the side chain make a hydrogen bond with Asp376. A covalent bond forms between the imidazole nitrogen of His231 and the carbon of the epoxide. The oxygen that is released from the breaking of the epoxide is coordinated with cobalt and occupies the cobalt-water position in the uncomplexed structure. A water eqidistant from both cobalts forms a hydrogen bond with this fumagillin oxygen. His339 rotates it side chain to avoid contact with fumagillin. The epoxide bearing side chain of fumagillin resembles methionine's side chain and the opened epoxide acts as a nucleophile on the carboxyl bond fulfilling the role of the water molecule allowing its entrance into the binding pocket.
MetAp-2 protein contains two domains, one that is 232 amino acids long and another that is 79 amino acids long. The CATH classification of these domains are as follows:
232: Class: alpha beta, Architecture: complex, Topology: creatine amidinohydrolase, Homology: Creatinase/methionine aminopeptidase superfamily
79: Class: mainly alpha Architecture: orthogonal bundle, Topology: arc receptor mutant, subunit A, Homology: "winged helix" repressor DNA binding domain