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PDBsum entry 1sgk

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protein links
Toxin PDB id
1sgk
Jmol
Contents
Protein chain
523 a.a.
Waters ×357
PDB id:
1sgk
Name: Toxin
Title: Nucleotide-free diphtheria toxin
Structure: Diphtheria toxin (dimeric). Chain: a. Synonym: dt. Ec: 2.4.2.36
Source: Corynephage beta. Organism_taxid: 10703. Other_details: purchased from connaught laboratories
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.182     R-free:   0.282
Authors: C.E.Bell,D.Eisenberg
Key ref:
C.E.Bell and D.Eisenberg (1997). Crystal structure of nucleotide-free diphtheria toxin. Biochemistry, 36, 481-488. PubMed id: 9012663 DOI: 10.1021/bi962214s
Date:
12-Sep-96     Release date:   23-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00588  (DTX_CORBE) -  Diphtheria toxin
Seq:
Struc:
 
Seq:
Struc:
567 a.a.
523 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.36  - NAD(+)--diphthamide ADP-ribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
NAD(+)
+ diphthamide-[translation elongation factor 2]
= nicotinamide
+ N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi962214s Biochemistry 36:481-488 (1997)
PubMed id: 9012663  
 
 
Crystal structure of nucleotide-free diphtheria toxin.
C.E.Bell, D.Eisenberg.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19421996 E.Krissinel (2010).
Crystal contacts as nature's docking solutions.
  J Comput Chem, 31, 133-143.  
11859081 M.P.Rosconi, and E.London (2002).
Topography of helices 5-7 in membrane-inserted diphtheria toxin T domain: identification and insertion boundaries of two hydrophobic sequences that do not form a stable transmembrane hairpin.
  J Biol Chem, 277, 16517-16527.  
10657208 R.K.Holmes (2000).
Biology and molecular epidemiology of diphtheria toxin and the tox gene.
  J Infect Dis, 181, S156-S167.  
9893993 J.Ren, J.C.Sharpe, R.J.Collier, and E.London (1999).
Membrane translocation of charged residues at the tips of hydrophobic helices in the T domain of diphtheria toxin.
  Biochemistry, 38, 976-984.  
9722516 K.Kachel, J.Ren, R.J.Collier, and E.London (1998).
Identifying transmembrane states and defining the membrane insertion boundaries of hydrophobic helices in membrane-inserted diphtheria toxin T domain.
  J Biol Chem, 273, 22950-22956.  
  19079637 P.J.Berti, S.R.Blanke, and V.L.Schramm (1997).
Transition State Structure for the Hydrolysis of NAD Catalyzed by Diphtheria Toxin.
  J Am Chem Soc, 119, 12079-12088.  
9312118 Y.Wang, S.E.Malenbaum, K.Kachel, H.Zhan, R.J.Collier, and E.London (1997).
Identification of shallow and deep membrane-penetrating forms of diphtheria toxin T domain that are regulated by protein concentration and bilayer width.
  J Biol Chem, 272, 25091-25098.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.