1SGK

NUCLEOTIDE-FREE DIPHTHERIA TOXIN

Summary for 1SGK

• Entry DOI: 10.2210/pdb1sgk/pdb
• Descriptor: DIPHTHERIA TOXIN (DIMERIC) (2 entities in total)
• Functional Keywords: toxin, adp-ribosylation, transferase, glycosyltransferase, nad, adp-ribosyl transferase
• Biological source: Corynephage beta
• Total number of polymer chains: 1
• Total formula weight: 58411.36

Authors

Bell, C.E.,Eisenberg, D. (deposition date: 1996-09-12, release date: 1996-12-23, Last modification date: 2024-10-30)

Primary citation

Bell, C.E.,Eisenberg, D.
Crystal structure of nucleotide-free diphtheria toxin.
Biochemistry, 36:481-488, 1997

PubMed Abstract: The crystal structure of diphtheria toxin (DT) in the absence of nucleotide (nucleotide-free DT) has been determined at 2.3 A resolution to a crystallographic R factor and free R factor of 18.2 and 28.2%, respectively. A comparison of this structure to the previously determined structures of DT in complex with adenyly(3'-5')uridine monophosphate (ApUp) and DT in complex with nicotinamide adenine dinucleotide (NAD) reveals that there are no significant movements of the two subdomains of the catalytic (C) domain associated with dinucleotide binding. The side chains of six residues within the active-site cleft, including Tyr65, Pro38, Tyr27, Thr23, Glu148, and Tyr54, show movements of up to 3 A upon dinucleotide binding. In the structure of nucleotide-free DT, the active-site loop residues 39-47 of the C domain are well ordered and extend over the active-site cleft in approximately the same position as in the structure of DT in complex with ApUp. This is in contrast to the structure of the DT-NAD complex, in which the active-site loop is disordered. On the basis of a comparison of the nucleotide-free and NAD-bound DT structures, we suggest that the interaction of NAD with Pro38 and also possibly Tyr54 and Trp153 could disrupt the network of hydrogen bonds that stabilizes the position of the active-site loop over the active-site cleft, allowing this loop to become disordered. This may be an important step in binding of the C domain of DT to its substrate, elongation factor-2.

PubMed: 9012663
DOI: 10.1021/bi962214s

Experimental method

X-RAY DIFFRACTION (2.3 Å)