3WT4

Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa

Summary for 3WT4

• Entry DOI: 10.2210/pdb3wt4/pdb
• Related: 4NJQ 4OID 4OIW
• Descriptor: Probable M18 family aminopeptidase 2, ZINC ION, CARBONATE ION, ... (4 entities in total)
• Functional Keywords: aspartyl aminopeptidase, tet shape protease, dodecameric peptidase, dodecameric tetraheral shape, hydrolase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 4
• Total formula weight: 187617.00

Authors

Nguyen, D.D.,Pandian, R.,Kim, D.D.,Ha, S.C.,Yoon, H.J.,Kim, K.S.,Yun, K.H.,Kim, J.H.,Kim, K.K. (deposition date: 2014-04-07, release date: 2014-04-16, Last modification date: 2024-03-20)

Primary citation

Nguyen, D.D.,Pandian, R.,Kim, D.,Ha, S.C.,Yoon, H.J.,Kim, K.S.,Yun, K.H.,Kim, J.H.,Kim, K.K.
Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa
Biochem.Biophys.Res.Commun., 447:101-107, 2014

PubMed Abstract: The peptidases in clan MH are known as cocatalytic zinc peptidases that have two zinc ions in the active site, but their metal preference has not been rigorously investigated. In this study, the molecular basis for metal preference is provided from the structural and biochemical analyses. Kinetic studies of Pseudomonas aeruginosa aspartyl aminopeptidase (PaAP) which belongs to peptidase family M18 in clan MH revealed that its peptidase activity is dependent on Co(2+) rather than Zn(2+): the kcat (s(-1)) values of PaAP were 0.006, 5.10 and 0.43 in no-metal, Co(2+), and Zn(2+)conditions, respectively. Consistently, addition of low concentrations of Co(2+) to PaAP previously saturated with Zn(2+) greatly enhanced the enzymatic activity, suggesting that Co(2+)may be the physiologically relevant cocatalytic metal ion of PaAP. The crystal structures of PaAP complexes with Co(2+) or Zn(2+) commonly showed two metal ions in the active site coordinated with three conserved residues and a bicarbonate ion in a tetragonal geometry. However, Co(2+)- and Zn(2+)-bound structures showed no noticeable alterations relevant to differential effects of metal species, except the relative orientation of Glu-265, a general base in the active site. The characterization of mutant PaAP revealed that the first metal binding site is primarily responsible for metal preference. Similar to PaAP, Streptococcus pneumonia glutamyl aminopeptidase (SpGP), belonging to aminopeptidase family M42 in clan MH, also showed requirement for Co(2+) for maximum activity. These results proposed that clan MH peptidases might be a cocatalytic cobalt peptidase rather than a zinc-dependent peptidase.

PubMed: 24704201
DOI: 10.1016/j.bbrc.2014.03.109

Experimental method

X-RAY DIFFRACTION (2.3 Å)