6J9D

Babesia microti lactate dehydrogenase R99A (BmLDHR99A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures ofBabesia microtilactate dehydrogenase BmLDH reveal a critical role for Arg99 in catalysis.

Yu, L.Shen, Z.Liu, Q.Zhan, X.Luo, X.An, X.Sun, Y.Li, M.Wang, S.Nie, Z.Ao, Y.Zhao, Y.Peng, G.Mamoun, C.B.He, L.Zhao, J.

(2019) FASEB J 33: 13669-13682

  • DOI: 10.1096/fj.201901259R
  • Primary Citation of Related Structures:  
    6J9D, 6K13, 6K12

  • PubMed Abstract: 
  • The tick- and transfusion-transmitted human pathogen Babesia microti infects host erythrocytes to cause the pathologic symptoms associated with human babesiosis, an emerging disease with worldwide distribution and potentially fatal clinical ...

    The tick- and transfusion-transmitted human pathogen Babesia microti infects host erythrocytes to cause the pathologic symptoms associated with human babesiosis, an emerging disease with worldwide distribution and potentially fatal clinical outcome. Drugs currently recommended for the treatment of babesiosis are associated with a high failure rate and significant adverse events, highlighting the urgent need for more-effective and safer babesiosis therapies. Unlike other apicomplexan parasites, B. microti lacks a canonical lactate dehydrogenase (LDH) but instead expresses a unique enzyme, B. microti LDH (BmLDH), acquired through evolution by horizontal transfer from a mammalian host. Here, we report the crystal structures of BmLDH in apo state and ternary complex (enzyme-NADH-oxamate) solved at 2.79 and 1.89 Å. Analysis of these structures reveals that upon binding to the coenzyme and substrate, the active pocket of BmLDH undergoes a major conformational change from an opened and disordered to a closed and stabilized state. Biochemical assays using wild-type and mutant B. microti and human LDHs identified Arg99 as a critical residue for the catalytic activity of BmLDH but not its human counterpart. Interestingly, mutation of Arg99 to Ala had no impact on the overall structure and affinity of BmLDH to NADH but dramatically altered the closure of the enzyme's active pocket. Together, these structural and biochemical data highlight significant differences between B. microti and human LDH enzymes and suggest that BmLDH could be a suitable target for the development of selective antibabesial inhibitors.-Yu, L., Shen, Z., Liu, Q., Zhan, X., Luo, X., An, X., Sun, Y., Li, M., Wang, S., Nie, Z., Ao, Y., Zhao, Y., Peng, G., Ben Mamoun, C., He, L., Zhao, J. Crystal structures of Babesia microti lactate dehydrogenase BmLDH reveal a critical role for Arg99 in catalysis.


    Organizational Affiliation

    Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenaseAB309Babesia microti strain RIMutation(s): 1 
Gene Names: BMR1_01G00020
EC: 1.1.1.27
Find proteins for I7J7V6 (Babesia microti (strain RI))
Explore I7J7V6 
Go to UniProtKB:  I7J7V6
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.332α = 90
b = 147.332β = 90
c = 65.773γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-01-22 
  • Released Date: 2019-10-16 
  • Deposition Author(s): Yu, L.

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references