4ND2

Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic acid) and cofactor analog (3-acetylpyridine adenine dinucleotide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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.,Instituto de BioquĂ­mica Vegetal y Fotosintesis (CSIC/U. Sevilla), Avda. Americo Vespucio 49, Seville 41092, Spain.,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
A, B
321Cryptosporidium parvum (strain Iowa II)Mutation(s): 0 
Find proteins for Q5CYZ2 (Cryptosporidium parvum (strain Iowa II))
Go to UniProtKB:  Q5CYZ2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3D
Query on A3D

Download SDF File 
Download CCD File 
A, B
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
C22 H28 N6 O14 P2
KPVQNXLUPNWQHM-RBEMOOQDSA-N
 Ligand Interaction
PYR
Query on PYR

Download SDF File 
Download CCD File 
A, B
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.830α = 90.00
b = 95.830β = 90.00
c = 185.640γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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