NADP+ Expels both the Co-factor and a Substrate Analog from the Mycobacterium tuberculosis ThyX Active Site: Opportunities for Anti-bacterial Drug Design

Parthasarathy Sampathkumar, Stewart Turley, Carol Hopkins Sibley, Wim G J Hol

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

The novel flavin-dependent thymidylate synthase, ThyX, is absent in humans but several pathogenic bacteria depend exclusively on ThyX activity to synthesize thymidylate. Reduction of the enzyme-bound FAD by NADPH is suggested to be the critical first step in ThyX catalysis. We soaked Mycobacterium tuberculosis ThyX-FAD-BrdUMP ternary complex crystals in a solution containing NADP+ to gain structural insights into the reductive step of the catalytic cycle. Surprisingly, the NADP+ displaced both FAD and BrdUMP from the active site. In the resultant ThyX-NADP+ binary complex, the AMP moiety is bound in a deep pocket similar to that of the same moiety of FAD in the ternary complex, while the nicotinamide part of NADP+ is engaged in a limited number of contacts with ThyX. The additional 2′-phosphate group attached to the AMP ribose of NADP+ could be accommodated with minor rearrangement of water molecules. The newly introduced 2′-phosphate groups are engaged in water-mediated interactions across the non-crystallographic 2-fold axis of the ThyX tetramer, suggesting possibilities for design of high-affinity bivalent inhibitors of this intriguing enzyme.

Original languageEnglish (US)
Pages (from-to)1-6
Number of pages6
JournalJournal of Molecular Biology
Volume360
Issue number1
DOIs
StatePublished - Jun 30 2006
Externally publishedYes

Fingerprint

Drug Design
NADP
Mycobacterium tuberculosis
Catalytic Domain
Flavin-Adenine Dinucleotide
Adenosine Monophosphate
Phosphates
Thymidylate Synthase
Ribose
Niacinamide
Water
Enzyme Inhibitors
Catalysis
Bacteria
Enzymes

Keywords

  • bivalent drugs
  • flavin
  • inhibitor design
  • thymidylate synthase

ASJC Scopus subject areas

  • Virology

Cite this

NADP+ Expels both the Co-factor and a Substrate Analog from the Mycobacterium tuberculosis ThyX Active Site : Opportunities for Anti-bacterial Drug Design. / Sampathkumar, Parthasarathy; Turley, Stewart; Sibley, Carol Hopkins; Hol, Wim G J.

In: Journal of Molecular Biology, Vol. 360, No. 1, 30.06.2006, p. 1-6.

Research output: Contribution to journalArticle

Sampathkumar, Parthasarathy ; Turley, Stewart ; Sibley, Carol Hopkins ; Hol, Wim G J. / NADP+ Expels both the Co-factor and a Substrate Analog from the Mycobacterium tuberculosis ThyX Active Site : Opportunities for Anti-bacterial Drug Design. In: Journal of Molecular Biology. 2006 ; Vol. 360, No. 1. pp. 1-6.
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