The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica.
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Citations
Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril.
Use of magnetic circular dichroism to study dinuclear metallohydrolases and the corresponding biomimetics
Heterologous expression and purification of Vibrio proteolyticus (Aeromonas proteolytica) aminopeptidase: a rapid protocol
P1′ Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases
The soluble domains of Gpi8 and Gaa1, two subunits of glycosylphosphatidylinositol transamidase (GPI-T), assemble into a complex
References
Processing of X-ray diffraction data collected in oscillation mode
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
SHELXL: high-resolution refinement.
Recent Advances in Zinc Enzymology
Automated refinement of protein models.
Related Papers (5)
The aminopeptidase from Aeromonas proteolytica: structure and mechanism of co-catalytic metal centers involved in peptide hydrolysis
Frequently Asked Questions (17)
Q2. What are the contributions mentioned in the paper "The high-resolution structures of the neutral and the low ph crystals of aminopeptidase from <em>aeromonas proteolytica</em>" ?
Herein the authors report the crystal structures of AAP at 0. 95-Å resolution at neutral pH and at 1. 24-Å resolution at low pH.
Q3. What was the use of CNS for the refinement of the structure?
The refinement program, CNS, was used for a rigid-body refinement using reflections from 30.0- to 4.0-Å resolution range and for several rounds of isotropic positional refinement using incrementally higher resolution data to 1.20 Å (1.24 Å for the low pH structure).
Q4. Why were the positions of all the atoms not restrained during refinement?
Because the positions of all the atoms were not restrained during refinement, precise Zn–ligand and C–O distances could be obtained without bias.
Q5. How does His256 shift away from the center of the active site?
To make way for the Zn1 movement, His256 shifts away from the center of the active site by 0.06 Å and rotates 2° around the C α –C β bond.
Q6. What is the corresponding lack of electron density for hydrogen atoms?
The lack of electron density corresponding to hydrogen atoms is expected for the side chain oxygen atoms of aspartic acid and glutamic acid, and the nitrogen of histidine ligands, since their side chains are within the first and second coordination spheres of the two metal ions and the pH is above the individual pK as for the liganded amino acid side chains.
Q7. What is the likely candidate to function as the nucleophile?
The reaction mechanism step at which deprotonation of the bridging solvent molecule occurs, the most likely candidate to function as the nucleophile, is unknown.
Q8. What is the likely cause of the increase in the Zn1–O coordination distance?
The increase in the Zn1–O coordination distance may be the result of adding a proton to the bridging hydroxide ion, the change in the coordination number of Zn1 from 4 to 5, or both.
Q9. What was the scale factor for the high-resolution data set?
The scale factor for the final image of the high-resolution data set was 0.72, while that for the low-resolution data set was 1.32.
Q10. What is the average B iso value for all active-site amino acids?
The average B iso value for all of the active-site amino acids is 7.17 Å2 compared with 10.85 Å2 for all protein atoms, indicating the active-site amino acids are slightly more rigid with respect to the rest of the enzyme.
Q11. How many peaks were associated with side chain carbons?
For the 30 identical peaks, 21 were associated with side chain carbons while only five were associated with C α and four with backbone nitrogen atoms.
Q12. How many peaks were identified as potential hydrogen atoms?
At 0.95-Å resolution 237 peaks (approximately 100 more peaks than were found at 1.20-Å resolution) were identified as potential hydrogen atoms with 30 peaks previously identified at 1.20-Å resolution.
Q13. What is the average Zn–O distance in the first coordination sphere?
The average Zn–N distance in the first coordination sphere of both metal ions is 2.03 Å and the average Zn–O distance is 2.07 Å, while in the second coordination sphere the average Zn–O distance is 2.39 Å (Table 3).
Q14. What is the average Zn–O distance for the bridging oxygen species?
The Zn–O distances for the bridging oxygen species in this structure are 2.01 Å to Zn1 and 1.93 Å to Zn2, suggesting the bridging oxygen species is an OH−.
Q15. What is the average B iso value for the ligands to Zn2?
The side chain residues liganded to Zn1 have an average B iso value of 8.47 Å2, which is significantly higher than the average B iso value for the ligands to Zn2 (7.01 Å2).
Q16. What is the role of Zn(II) ions in the catalytic process?
Definitive assignment of the roles of each of the Zn(II) ions awaits a high-resolution structure of a productive enzyme–substrate complex, a difficult but worthwhile goal for this class of enzyme.
Q17. What is the optimum distance of the metal ions to their ligands?
During the course of the enzymatic reaction, the distances of the metal ions to their ligands may change in accordance with the chemical state of the substrate/intermediate.