4ND4

Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic acid) and cofactor (b-nicotinamide adenine dinucleotide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.

Cook, W.J.Senkovich, O.Hernandez, A.Speed, H.Chattopadhyay, D.

(2014) Int J Biol Macromol 74C: 608-619

  • DOI: 10.1016/j.ijbiomac.2014.12.019
  • Primary Citation of Related Structures:  
    4ND1, 4ND2, 4ND3, 4ND4, 4ND5

  • PubMed Abstract: 
  • The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis ...

    The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes.


    Organizational Affiliation

    Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States. Electronic address: debasish@uab.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenaseA, B321Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: cgd7_480LDH1
EC: 1.1.1.27
UniProt
Find proteins for Q5CYZ2 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CYZ2 
Go to UniProtKB:  Q5CYZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CYZ2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.905α = 90
b = 95.905β = 90
c = 185.723γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description