Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.4.11.18 (MAP)
 7,412 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

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.
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PMID:Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. 952 Mar 90

By improving the expression and purification of Escherichia coli methionine aminopeptidase (eMetAP) and using slightly different crystallization conditions, the resolution of the parent structure was extended from 2.4 to 1.9 A resolution. This has permitted visualization of the coordination geometry and solvent structure of the active-site dinuclear metal center. One solvent molecule (likely a mu-hydroxide) bridges the trigonal bipyramidal (Co1) and octahedral (Co2) cobalt ions. A second solvent (possibly a hydroxide ion) is bound terminally to Co2. A monovalent cation binding site was also identified about 13 A away from the metal center at an interface between the two subdomains of the protein. The first structure of a substrate-like inhibitor, (3R)-amino-(2S)-hydroxyheptanoyl-L-Ala-L-Leu-L-Val-L-Phe-OMe, bound to a methionine aminopeptidase, has also been determined. This inhibitor coordinates the metal center through four interactions as follows: (i) ligation of the N-terminal (3R)-nitrogen to Co2, (ii, iii) bridging coordination of the (2S)-hydroxyl group, and (iv) terminal ligation to Co1 by the keto oxygen of the pseudo-peptide linkage. Inhibitor binding occurs with the displacement of two solvent ligands and the expansion of the coordination sphere of Co1. In addition to the tetradentate, bis-chelate metal coordination, the substrate analogue forms hydrogen bonds with His79 and His178, two conserved residues within the active site of all MetAPs. To evaluate their importance in catalysis His79 and His178 were replaced with alanine. Both substitutions, but especially that of His79, reduce activity. The structure of the His79Ala apoenzyme and the comparison of its electronic absorption spectra with other variants suggest that the loss in activity is not due to a conformational change or a defective metal center. Two different reaction mechanisms are proposed and are compared to those of related enzymes. These results also suggest that inhibitors analogous to that reported here may be useful in preventing angiogenesis in cancer and in the treatment of microbial and fungal infections.
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PMID:Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis. 1038 7

Enhanced biological phosphorus removal wastewater treatment plants that use anaerobic digesters for sludge treatment, have high phosphorus concentrations in the sidestreams from their sludge dewatering equipment. To remove phosphorus from such sidestreams controlled struvite crystallisation can be used. Struvite (or MAP) is a naturally occurring crystal of magnesium, ammonium and phosphate. We present operational results obtained with a continuously operated pilot-scale MAP reactor. The pilot-scale reactor (143 l) was an air agitated column reactor with a reaction and a settling zone, based on the Phosnix process of Unitika Ltd., Japan. The influent to the MAP reactor was centrate from the centrifuge that dewaters anaerobically digested sludge at the Oxley Creek wastewater treatment plant in Brisbane. We used a 60% magnesium hydroxide slurry to add the required magnesium to the process and to obtain the alkaline pH value required. The pilot-scale MAP process achieved an ortho-P removal ratio of 94% from an average influent ortho-P concentration of 61 mg/l. The reactor was operated at a pH of around 8.5. Insufficient dosing of magnesium reduced the P removal performance. There was no influence of the hydraulic residence time on the process in the range of 1-8 h. The dry MAP product had cadmium, lead and mercury concentrations well below the legal limits for fertilisers in Queensland, Australia and can be reused as a valuable slow-release fertiliser.
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PMID:Controlled struvite crystallisation for removing phosphorus from anaerobic digester sidestreams. 1125 69

Streptomyces griseus aminopeptidase (SGAP) is a double-zinc exopeptidase with a high preference toward large hydrophobic amino-terminus residues. It is a monomer of a relatively low molecular weight (30 kDa), it is heat stable, it displays a high and efficient catalytic turnover, and its activity is modulated by calcium ions. The small size, high activity, and heat stability make SGAP a very attractive enzyme for various biotechnological applications, among which is the processing of recombinant DNA proteins and fusion protein products. Several free amino acids, such as phenylalanine, leucine, and methionine, were found to act as weak inhibitors of SGAP and hence were chosen for structural studies. These inhibitors can potentially be regarded as product analogs because one of the products obtained in a normal enzymatic reaction is the cleaved amino terminal amino acid of the substrate. The current study includes the X-ray crystallographic analysis of the SGAP complexes with methionine (1.53 A resolution), leucine (1.70 A resolution), and phenylalanine (1.80 A resolution). These three high-resolution structures have been used to fully characterize the SGAP active site and to identify some of the functional groups of the enzyme that are involved in enzyme-substrate and enzyme-product interactions. A unique binding site for the terminal amine group of the substrate (including the side chains of Glu131 and Asp160, as well as the carbonyl group of Arg202) is indicated to play an important role in the binding and orientation of both the substrate and the product of the catalytic reaction. These studies also suggest that Glu131 and Tyr246 are directly involved in the catalytic mechanism of the enzyme. Both of these residues seem to be important for substrate binding and orientation, as well as the stabilization of the tetrahedral transition state of the enzyme-substrate complex. Glu131 is specifically suggested to function as a general base during catalysis by promoting the nucleophilic attack of the zinc-bound water/hydroxide on the substrate carbonyl carbon. The structures of the three SGAP complexes are compared with recent structures of three related aminopeptidases: Aeromonas proteolytica aminopeptidase (AAP), leucine aminopeptidase (LAP), and methionine aminopeptidase (MAP) and their complexes with corresponding inhibitors and analogs. These structural results have been used for the simulation of several species along the reaction coordinate and for the suggestion of a general scheme for the proteolytic reaction catalyzed by SGAP.
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PMID:Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism. 1148 27

1. 3-Hydroxy-3-methylglutaryl co-enzyme A reductase inhibitors (statins) prevent the progression of atherosclerosis by lowering cholesterol. However, the effect of statins on the synthesis of pro-inflammatory cytokines from endothelial cells has not yet been fully investigated. Here, we examined the effect of pravastatin, one of the statins, on IL-8 synthesis induced by thrombin in human aortic endothelial cells (AoEC) cultured with high glucose concentrations. 2. Pravastatin significantly decreased the IL-8 synthesis induced by thrombin. 3. Pravastatin inhibited the p44/42 MAP kinase activity induced by thrombin, but did not inhibit the p38 MAP kinase activity. 4. Translocation of ras protein from the cytosol to plasma membrane was inhibited by pravastatin. 5. Pravastatin inhibit the activator protein-1 activity, but did not inhibit the activation of IkappaB-alpha. 6. Dominant negative ras inhibited the p44/42 MAP kinase activity induced by PMA. 7. Our results suggest that pravastatin inhibits IL-8 synthesis by blocking the ras-MAP (p44/42) kinase pathway rather than nuclear factor-kappaB. Pravastatin may prevent atherosclerosis not only by lowering cholesterol levels, but also by suppressing IL-8 synthesis in AoEC through the inhibition of p44/42 MAP kinase, and this may be more beneficial in diabetic patients than in non-diabetics.
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PMID:Pravastatin suppresses the interleukin-8 production induced by thrombin in human aortic endothelial cells cultured with high glucose by inhibiting the p44/42 mitogen activated protein kinase. 1160 15

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co2+ ions or Zn2+ ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. coli methionine aminopeptidase type I (eMetAP- 1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.
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PMID:Investigation of the metal binding site in methionine aminopeptidase by density functional theory. 1236 16

The structure of prolidase from the hyperthermophilic archaeon Pyrococcus furiosus (Pfprol) has been solved and refined at 2.0 A resolution. This is the first structure of a prolidase, i.e., a peptidase specific for dipeptides having proline as the second residue. The asymmetric unit of the crystals contains a homodimer of the enzyme. Each of the two protein subunits has two domains. The C-terminal domain includes the catalytic site, which is centered on a dinuclear metal cluster. In the as-isolated form of Pfprol, the active-site metal atoms are Co(II) [Ghosh, M., et al. (1998) J. Bacteriol. 180, 4781-9]. An unexpected finding is that in the crystalline enzyme the active-site metal atoms are Zn(II), presumably as a result of metal exchange during crystallization. Both of the Zn(II) atoms are five-coordinate. The ligands include a bridging water molecule or hydroxide ion, which is likely to act as a nucleophile in the catalytic reaction. The two-domain polypeptide fold of Pfprol is similar to the folds of two functionally related enzymes, aminopeptidase P (APPro) and creatinase. In addition, the catalytic C-terminal domain of Pfprol has a polypeptide fold resembling that of the sole domain of a fourth enzyme, methionine aminopeptidase (MetAP). The active sites of APPro and MetAP, like that of Pfprol, include a dinuclear metal center. The metal ligands in the three enzymes are homologous. Comparisons with the molecular structures of APPro and MetAP suggest how Pfprol discriminates against oligopeptides and in favor of Xaa-Pro substrates. The crystal structure of Pfprol was solved by multiple-wavelength anomalous dispersion. The crystals yielded diffraction data of relatively high quality and resolution, despite the fact that one of the two protein subunits in the asymmetric unit was found to be significantly disordered. The final R and R(free) values are 0.24 and 0.28, respectively.
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PMID:Structure of the prolidase from Pyrococcus furiosus. 1500 12

The catalytic hydrolysis of a methionyl-peptide substrate by a methionine aminopeptidase active site model cluster was investigated at the DF/B3LYP level of theory, in the gas-phase and in the protein environment. Zn(II), Co(II), Mn(II), and Fe(II) transition metals were examined as the potential catalytic metals of this enzyme involved in protein maturation. Two different mechanisms in which Glu204 was present as protonated or deprotonated residue were considered. The energetic profiles show lower barriers as the protonated glutamate is involved. The rate-determining step of the hydrolysis reaction is always the nucleophilic addition of the hydroxide on substrate carbon, followed by less energetically demanding methionine-peptide C-N bond scission. The lowest activation energy is obtained in the case of zinc dication while the other metals show very high energetic barriers, so that methionine aminopeptidase can be in principle recognized as a dizinc enzyme.
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PMID:Which one among Zn(II), Co(II), Mn(II), and Fe(II) is the most efficient ion for the methionine aminopeptidase catalyzed reaction? 1752 36

The dicobalt form of the metallohydrolase methionine aminopeptidase from Escherichia coli (CoCo EcMetAP) has an active site with one 5-coordinate Co (II) and a more weakly bound 6-coordinate Co (II). These metal ions are bridged by two carboxylate amino acid side chains and water or hydroxide, potentially enabling magnetic exchange coupling between the metals. We used variable-temperature, variable-field magnetic circular dichroism to determine whether such coupling occurs. CoCo EcMetAP's MCD spectrum shows distinct d-d transitions at 495 and 567 nm caused by 6- and 5-coordinate Co (II), respectively. The magnetization curves for 5- and 6-coordinate Co (II) are very different, indicating that their electronic ground states vary considerably, ruling out any coupling. When the fungal metabolite fumagillin binds to the CoCoEcMetAP, the qualitative MCD spectrum is unchanged; however, VTVH MCD data show that 5- and 6-coordinate Co (II) ions have similarly shaped magnetization curves, indicating that the Co (II) ions now share the same electronic ground state. Fitting the VTVH MCD data to a model in which dimer wave functions are calculated using a spin Hamiltonian with zero-field splitting showed the Co (II) ions to be weakly ferromagnetically coupled, with J = 2.9 cm (-1). Ferromagnetic coupling is unusual for dinuclear Co (II); therefore, to support the CoCoEcMetAP/fumagillin complex results, we also analyzed VTVH MCD data from a matched pair of dinuclear cobalt complexes, 1 and 2. Complex 1 shares the carboxylate and hydroxide-bridged dicobalt(II) structural motif with the active site of CoCo EcMetAP. Complex 2 contains a nearly isostructural Co (II) ion, but the Co (III) is diamagnetic, so any magnetic coupling is switched off, while the spectral features of the Co (II) ion remain. Magnetization data for 1, fitted to the dimer model, showed that the Co (II) ions were weakly ferromagnetically coupled, with J = 1.7 cm (-1). Magnetization data for Co (II) ions in 2, however, reflect loss of magnetic exchange coupling.
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PMID:Magnetic circular dichroism study of a dicobalt(II) methionine aminopeptidase/fumagillin complex and dicobalt II-II and II-III model complexes. 1892 93

The magnetic circular dichroism (MCD) study of [Co(2)(mu-OH)(mu-Ph(4)DBA)(TMEDA)(2)(OTf)], in which Ph(4)DBA is the dinucleating bis(carboxylate) ligand dibenzofuran-4,6-bis(diphenylacetate) and TMEDA is N,N,N',N'-tetramethylethylenediamine, is presented. This complex serves as an excellent spectroscopic model for a number of dicobalt(II) enzymes and proteins that have both the mu-hydroxo, mu-carboxylato bridging and asymmetric 6- and 5-coordination. The low-temperature MCD spectrum of the model complex shows bands at 490, 504, and 934 nm arising from d-d transitions on the 6-coordinate Co(II) and bands at 471, 522, 572, 594, and 638 nm arising from d-d transitions on the 5-coordinate Co(II). The most intense MCD bands are at 504 and 572 nm for 6- and 5-coordinate Co(II), respectively, and these two bands are found in the MCD spectra of dicobalt(II)-substituted methionine aminopeptidase from Escherichia coli (CoCoMetAP), glycerophosphodiesterase from Enterobacter aerogenes (CoCoGpdQ), aminopeptidase from Aeromonas proteolytica (CoCoAAP), and myohemerythrin from Themiste zostericola (CoCoMyoHry). These dicobalt(II)-substituted proteins are known to have one 5- and one 6-coordinate Co(II) bridged by one or two carboxylates and either a water or a hydroxide. The uncertainty of the bridging water's state of protonation is problematic, as this is a likely candidate for the attacking nucleophile in the dimetallohydrolases. Analysis of the variable-temperature variable-field (VTVH) MCD data determined that the Co(II) ions in the model complex are ferromagnetically coupled with a J of 3.0 cm(-1). A comparison of all dicobalt(II) complexes and dicobalt(II)-substituted protein active sites with the mu-hydroxo/aqua, mu-carboxylato bridging motif reveals that J is either zero or negative (antiferromagnetic) in the mu-aqua systems and positive (ferromagnetic) in the mu-hydroxo systems. It was also determined that the Co(II) ions in CoCoAAP and CoCoMyoHry are ferromagnetically coupled, each with a J of 3.4 cm(-1), which suggests that these ions have a mu-hydroxo bridging ligand.
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PMID:Magnetic circular dichroism study of a dicobalt(II) complex with mixed 5- and 6-coordination: a spectroscopic model for dicobalt(II) hydrolases. 1969 27


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