7K5K | pdb_00007k5k

Plasmodium vivax M17 leucyl aminopeptidase Pv-M17


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7K5K

This is version 1.4 of the entry. See complete history

Literature

Active site metals mediate an oligomeric equilibrium in Plasmodium M17 aminopeptidases.

Malcolm, T.R.Belousoff, M.J.Venugopal, H.Borg, N.A.Drinkwater, N.Atkinson, S.C.McGowan, S.

(2020) J Biological Chem 296: 100173-100173

  • DOI: https://doi.org/10.1074/jbc.RA120.016313
  • Primary Citation Related Structures: 
    6WVV, 7K5K

  • PubMed Abstract: 

    M17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases from Plasmodium falciparum (PfA-M17) and Plasmodium vivax (Pv-M17) function as catalytically active hexamers to generate free amino acids from human hemoglobin and are drug targets for the design of novel antimalarial agents. However, the molecular basis for oligomeric assembly is not fully understood. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found that PfA-M17 and Pv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species that can be controlled by manipulating the identity and concentration of metals available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of Pv-M17 by cryoelectron microscopy and X-ray crystallography together with solution studies revealed that PfA-M17 and Pv-M17 bind metal ions and substrates in a conserved fashion, although Pv-M17 forms the active hexamer more readily and processes substrates faster than PfA-M17. On the basis of these studies, we propose a dynamic equilibrium between monomer ↔ dimer ↔ tetramer ↔ hexamer, which becomes directional toward the large oligomeric states with the addition of metal ions. This sophisticated metal-dependent dynamic equilibrium may apply to other M17 aminopeptidases and underpin the moonlighting capabilities of this enzyme family.


  • Organizational Affiliation
    • Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.

Macromolecule Content 

  • Total Structure Weight: 363.67 kDa 
  • Atom Count: 24,224 
  • Modeled Residue Count: 3,270 
  • Deposited Residue Count: 3,330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase, putative
A, B, C, D, E
A, B, C, D, E, F
555Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_120064700PVP01_1260800
EC: 3.4.11.1 (PDB Primary Data), 3.4.13 (UniProt)
UniProt
Find proteins for A5K3U9 (Plasmodium vivax (strain Salvador I))
Explore A5K3U9 
Go to UniProtKB:  A5K3U9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K3U9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO3

Query on CO3



Download:Ideal Coordinates CCD File
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
MN

Query on MN



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
K [auth B]
L [auth B]
N [auth C]
H [auth A],
I [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
W [auth F],
X [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1185354

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-07-21
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.4: 2025-05-21
    Changes: Data collection, Structure summary