7CMC

CRYSTAL STRUCTURE OF DEOXYHYPUSINE SYNTHASE FROM PYROCOCCUS HORIKOSHII

Replaces:  4P63

Summary for 7CMC

• Entry DOI: 10.2210/pdb7cmc/pdb
• Descriptor: Probable deoxyhypusine synthase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: deoxyhypusine synthase, if5a, nad+, transferase
• Biological source: Pyrococcus horikoshii OT3
• Total number of polymer chains: 4
• Total formula weight: 157579.11

Authors

Yu, J.,Gai, Z.Q.,Okada, C.,Yao, M. (deposition date: 2020-07-27, release date: 2020-09-02, Last modification date: 2023-11-29)

Primary citation

Chen, M.,Gai, Z.,Okada, C.,Ye, Y.,Yu, J.,Yao, M.
Flexible NAD+Binding in Deoxyhypusine Synthase Reflects the Dynamic Hypusine Modification of Translation Factor IF5A.
Int J Mol Sci, 21:-, 2020

PubMed Abstract: The eukaryotic and archaeal translation factor IF5A requires a post-translational hypusine modification, which is catalyzed by deoxyhypusine synthase (DHS) at a single lysine residue of IF5A with NAD and spermidine as cofactors, followed by hydroxylation to form hypusine. While human DHS catalyzed reactions have been well characterized, the mechanism of the hypusination of archaeal IF5A by DHS is not clear. Here we report a DHS structure from (DHS) at 2.2 Å resolution. The structure reveals two states in a single functional unit (tetramer): two NAD-bound monomers with the NAD and spermidine binding sites observed in multi-conformations (closed and open), and two NAD-free monomers. The dynamic loop region V288-P299, in the vicinity of the active site, adopts different positions in the closed and open conformations and is disordered when NAD is absent. Combined with NAD binding analysis, it is clear that DHS can exist in three states: apo, DHS-2 equiv NAD, and DHS-4 equiv NAD, which are affected by the NAD concentration. Our results demonstrate the dynamic structure of DHS at the NAD and spermidine binding site, with conformational changes that may be the response to the local NAD concentration, and thus fine-tune the regulation of the translation process via the hypusine modification of IF5A.

PubMed: 32752130
DOI: 10.3390/ijms21155509

Experimental method

X-RAY DIFFRACTION (2.2 Å)