3CH3

Crystal Structure Analysis of SERA5E from plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights into the Protease-like Antigen Plasmodium falciparum SERA5 and Its Noncanonical Active-Site Serine

Hodder, A.N.Malby, R.L.Clarke, O.B.Fairlie, W.D.Colman, P.M.Crabb, B.S.Smith, B.J.

(2009) J.Mol.Biol. 392: 154-165

  • DOI: 10.1016/j.jmb.2009.07.007
  • Primary Citation of Related Structures:  3CH2

  • PubMed Abstract: 
  • The sera genes of the malaria-causing parasite Plasmodium encode a family of unique proteins that are maximally expressed at the time of egress of parasites from infected red blood cells. These multi-domain proteins are unique, containing a central p ...

    The sera genes of the malaria-causing parasite Plasmodium encode a family of unique proteins that are maximally expressed at the time of egress of parasites from infected red blood cells. These multi-domain proteins are unique, containing a central papain-like cysteine-protease fragment enclosed between the disulfide-linked N- and C-terminal domains. However, the central fragment of several members of this family, including serine repeat antigen 5 (SERA5), contains a serine (S596) in place of the active-site cysteine. Here we report the crystal structure of the central protease-like domain of Plasmodium falciparum SERA5, revealing a number of anomalies in addition to the putative nucleophilic serine: (1) the structure of the putative active site is not conducive to binding substrate in the canonical cysteine-protease manner; (2) the side chain of D594 restricts access of substrate to the putative active site; and (3) the S(2) specificity pocket is occupied by the side chain of Y735, reducing this site to a small depression on the protein surface. Attempts to determine the structure in complex with known inhibitors were not successful. Thus, despite having revealed its structure, the function of the catalytic domain of SERA5 remains an enigma.


    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine-repeat antigen protein
X
265Plasmodium falciparumGene Names: SERA
Find proteins for Q9TY95 (Plasmodium falciparum)
Go to UniProtKB:  Q9TY95
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
X
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
2HP
Query on 2HP

Download SDF File 
Download CCD File 
X
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 103.368α = 90.00
b = 103.368β = 90.00
c = 72.508γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description