2WBF

Crystal Structure Analysis of SERA5E from plasmodium falciparum with loop 690-700 ordered


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 2.1 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:  
    2WBF, 3CH2, 3CH3

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE-REPEAT ANTIGEN PROTEINX265Plasmodium falciparumMutation(s): 0 
EC: 3.4.22
Find proteins for P69193 (Plasmodium falciparum (isolate CDC / Honduras))
Explore P69193 
Go to UniProtKB:  P69193
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download CCD File 
X
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.36α = 90
b = 102.36β = 90
c = 71.4γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-04-25
    Changes: Atomic model, Data collection, Database references, Source and taxonomy
  • Version 2.1: 2019-05-29
    Changes: Data collection, Experimental preparation