Dynamic conformations of the CD38-mediated NAD cyclization captured in a single crystal

Hongmin Zhang, Richard Graeff, Zhe Chen, Liangren Zhang, Lihe Zhang, Honcheung Lee, Quan Hao

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

The extracellular domain of human CD38 is a multifunctional enzyme involved in the metabolism of two Ca2+ messengers: cyclic ADP-ribose and nicotinic acid adenine dinucleotide phosphate. When NAD is used as substrate, CD38 predominantly hydrolyzes it to ADP-ribose, with a trace amount of cyclic ADP-ribose produced through cyclization of the substrate. However, mutation of a key residue at the active site, E146, inhibits the hydrolysis activity of CD38 but greatly increases its cyclization activity. To understand the role of the residue E146 in the catalytic process, we determined the crystal structure of the E146A mutant protein with a substrate analogue, arabinosyl-2′-fluoro- deoxy-nicotinamide adenine dinucleotide. The structure captured the enzymatic reaction intermediates in six different conformations in a crystallographic asymmetric unit. The structural results indicate a folding-back process for the adenine ring of the substrate and provide the first multiple snapshots of the process. Our approach of utilizing multiple molecules in the crystallographic asymmetric unit should be generally applicable for capturing the dynamic nature of enzymatic catalysis.

Original languageEnglish (US)
Pages (from-to)1070-1078
Number of pages9
JournalJournal of Molecular Biology
Volume405
Issue number4
DOIs
StatePublished - 2011
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported, in part, by National Institutes of Health grant GM061568 (to H.C.L. and Q.H.). This work was also supported by grants HKU 765909M , HKU 769107M , and N_HKU 722/08 from the Research Grant Council of Hong Kong and the National Science Foundation of China (to Q.H., H.C.L., and L.H.Z.). The crystallographic data were collected at the Shanghai Synchrotron Radiation Facility.

Keywords

  • ADP-ribose
  • ADPR
  • PDB
  • Protein Data Bank
  • ara-2′F-ADPR
  • ara-2′F-NAD
  • arabinosyl-2′-fluoro-deoxy-adenosine diphosphate-ribose
  • arabinosyl-2′-fluoro-deoxy-nicotinamide adenine dinucleotide
  • cADPR
  • cyclic ADP-ribose

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