6WVV

Plasmodium vivax M17 leucyl aminopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biol Chem 296: 100173-100173

  • DOI: https://doi.org/10.1074/jbc.RA120.016313
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
528Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_120064700PVP01_1260800
EC: 3.4.11.1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth E]
BA [auth B]
BB [auth E]
CB [auth E]
AA [auth B],
AB [auth E],
BA [auth B],
BB [auth E],
CB [auth E],
IB [auth F],
JA [auth C],
JB [auth F],
O [auth A],
PA [auth D],
PB [auth G],
WB [auth H]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EC [auth I]
FA [auth B]
FB [auth E]
GA [auth B]
HA [auth B]
EC [auth I],
FA [auth B],
FB [auth E],
GA [auth B],
HA [auth B],
KC [auth J],
NA [auth C],
NB [auth F],
NC [auth K],
QC [auth L],
RC [auth L],
TB [auth G],
UA [auth D],
UB [auth G],
V [auth A],
W [auth A],
X [auth A],
ZB [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AC [auth I]
BC [auth I]
CA [auth B]
FC [auth J]
GB [auth F]
AC [auth I],
BC [auth I],
CA [auth B],
FC [auth J],
GB [auth F],
GC [auth J],
HB [auth F],
HC [auth J],
IA [auth C],
KA [auth C],
KB [auth F],
M [auth A],
N [auth A],
OA [auth D],
OB [auth G],
P [auth A],
Q [auth A],
QA [auth D],
QB [auth G],
R [auth A],
RA [auth D],
S [auth A],
VA [auth E],
VB [auth H],
WA [auth E],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth B],
ZA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CC [auth I]
DA [auth B]
DB [auth E]
DC [auth I]
EA [auth B]
CC [auth I],
DA [auth B],
DB [auth E],
DC [auth I],
EA [auth B],
EB [auth E],
IC [auth J],
JC [auth J],
LA [auth C],
LB [auth F],
LC [auth K],
MA [auth C],
MB [auth F],
MC [auth K],
OC [auth L],
PC [auth L],
RB [auth G],
SA [auth D],
SB [auth G],
T [auth A],
TA [auth D],
U [auth A],
XB [auth H],
YB [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.035α = 90
b = 201.549β = 106.013
c = 166.224γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1185354

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: 2023-10-18
    Changes: Data collection, Database references, Refinement description