Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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Characterization of a New Member of the Flavoprotein Disulfide Reductase Family of Enzymes from Mycobacterium tuberculosis

Argyrou, A.Vetting, M.W.Blanchard, J.S.

(2004) J Biol Chem 279: 52694-52702

  • DOI: https://doi.org/10.1074/jbc.M410704200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The lpdA (Rv3303c) gene from Mycobacterium tuberculosis encoding a new member of the flavoprotein disulfide reductases was expressed in Escherichia coli, and the recombinant LpdA protein was purified to homogeneity. LpdA is a homotetramer and co-purifies with one molecule of tightly but noncovalently bound FAD and NADP+ per monomer. Although annotated as a probable lipoamide dehydrogenase in M. tuberculosis, LpdA cannot catalyze reduction of lipoyl substrates, because it lacks one of two cysteine residues involved in dithiol-disulfide interchange with lipoyl substrates and a His-Glu pair involved in general acid catalysis. The crystal structure of LpdA was solved by multiple isomorphous replacement with anomalous scattering, which confirmed the absence of these catalytic residues from the active site. Although LpdA cannot catalyze reduction of disulfide-bonded substrates, it catalyzes the NAD(P)H-dependent reduction of alternative electron acceptors such as 2,6-dimethyl-1,4-benzoquinone and 5-hydroxy-1,4-naphthaquinone. Significant primary deuterium kinetic isotope effects were observed with [4S-2H]NADH establishing that the enzyme promotes transfer of the C4-proS hydride of NADH. The absence of an isotope effect with [4S-2H]NADPH, the low Km value of 0.5 microm for NADPH, and the potent inhibition of the NADH-dependent reduction of 2,6-dimethyl-1,4-benzoquinone by NADP+ (Ki approximately 6 nm) and 2'-phospho-ADP-ribose (Ki approximately 800 nm), demonstrate the high affinity of LpdA for 2'-phosphorylated nucleotides and that the physiological substrate/product pair is NADPH/NADP+ rather than NADH/NAD+. Modeling of NADP+ in the active site revealed that LpdA achieves the high specificity for NADP+ through interactions involving the 2'-phosphate of NADP+ and amino acid residues that are different from those in glutathione reductase.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA. aargyrou@medusa.bioc.aecom.yu.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
499Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3303c - lpdA
Find proteins for P9WHH7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHH7 
Go to UniProtKB:  P9WHH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHH7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C27 H33 N9 O15 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 244.2α = 90
b = 244.2β = 90
c = 104.8γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations