1AKP

SEQUENTIAL 1H,13C AND 15N NMR ASSIGNMENTS AND SOLUTION CONFORMATION OF APOKEDARCIDIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Sequential 1H, 13C, and 15N NMR assignments and solution conformation of apokedarcidin.

Constantine, K.L.Colson, K.L.Wittekind, M.Friedrichs, M.S.Zein, N.Tuttle, J.Langley, D.R.Leet, J.E.Schroeder, D.R.Lam, K.S.Farmer III, B.T.Metzler, W.J.Bruccoleri, R.E.Mueller, L.

(1994) Biochemistry 33: 11438-11452


  • PubMed Abstract: 
  • Kedarcidin is a recently discovered antitumor antibiotic chromoprotein. The solution conformation of the kedarcidin apoprotein (114 residues) has been characterized by heteronuclear multidimensional NMR spectroscopy. Sequence-specific backbone atom r ...

    Kedarcidin is a recently discovered antitumor antibiotic chromoprotein. The solution conformation of the kedarcidin apoprotein (114 residues) has been characterized by heteronuclear multidimensional NMR spectroscopy. Sequence-specific backbone atom resonance assignments were obtained for a uniformly 13C/15N-enriched sample of apokedarcidin via a semiautomated analysis of 3D HNCACB, 3D CBCA-(CO)NH, 4D HNCAHA, 4D HN(CO)CAHA, 3D HBHA(CO)NH, and 3D HNHA(Gly) spectra. Side-chain assignments were subsequently obtained by analysis of (primarily) 3D HCCH-TOCSY and HCCH-COSY spectra. A qualitative analysis of the secondary structure is presented on the basis of 3J alpha NH coupling constants, deviations of 13C alpha and 13C beta chemical shifts from random coil values, and NOEs observed in 3D 15N- and 13C-edited NOESY-HSQC spectra. This analysis revealed a four-stranded antiparallel beta-sheet, a three-stranded antiparallel beta-sheet, and two two-standed antiparallel beta-sheets. The assignments of cross-peaks in the 3D NOESY spectra were assisted by reference to a preliminary model of apokedarcidin built using the program CONGEN starting from the X-ray structure of the homologous protein aponeocarzinostatin. An ensemble of 15 apokedarcidin solution structures has been generated by variable target function minimization (DIANA program) and refined by simulated annealing (X-PLOR program). The average backbone atom root-mean-square difference between the individual structures and the mean coordinates is 0.68 +/- 0.08 A. The overall fold of apokedarcidin is well-defined; it is composed of an immunoglobulin-like seven-stranded antiparallel beta-barrel and a subdomain containing two antiparallel beta-ribbons. Highly similar tertiary structures have been previously reported for the related proteins neocarzinostatin, macromomycin, and actinoxanthin. Important structural features are revealed, including the dimensions of the chromophore-binding pocket and the locations of side chains that are likely to be involved in chromophore stabilization.


    Related Citations: 
    • Chemistry and Structure Elucidation of the Kedarcidin Chromophore
      Leet, J.E.,Schroeder, D.R.,Langley, D.R.,Colson, K.L.,Huang, S.,Klohr, S.E.,Lee, M.S.,Golik, J.,Hofstead, S.J.,Doyle, T.W.,Matson, J.A.
      (1993) J.Am.Chem.Soc. 115: 8432
    • Kedarcidin, a New Chromoprotein Antitumor Antibiotic I. Taxonomy of Producing Organism, Fermentation and Biological Activity
      Lam, K.S.,Hesler, G.A.,Gustavson, D.R.,Crosswell, A.R.,Veitch, J.M.,Forenza, S.,Tomita, K.
      (1991) J.Antibiot. 44: 472
    • Selective Proteolytic Activity of the Antitumor Agent Kedarcidin
      Zein, N.,Casazza, A.M.,Doyle, T.W.,Leet, J.E.,Scheoeder, D.R.,Solomon, W.,Nadler, S.G.
      (1993) Proc.Natl.Acad.Sci.USA 90: 8009
    • Kedarcidin, a New Chromoprotein Antitumor Antibiotic. II. Isolation, Purification and Physico-Chemical Properties
      Hofstead, S.J.,Matson, J.A.,Malacko, A.R.,Marquart, H.
      (1992) J.Antibiot. 45: 1250
    • Kedarcidin Chromophore: An Enediyne that Cleaves DNA in a Sequence-Specific Manner
      Zein, N.,Colson, K.L.,Leet, J.E.,Schroeder, D.R.,Solomon, W.,Doyle, T.W.,Casazza, A.M.
      (1993) Proc.Natl.Acad.Sci.USA 90: 2822


    Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APOKEDARCIDIN
A
114Actinomycete sp. (strain L585-6 / ATCC 53650)N/A
Find proteins for P41249 (Actinomycete sp. (strain L585-6 / ATCC 53650))
Go to UniProtKB:  P41249
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 
  • Olderado: 1AKP Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-22
    Type: Database references
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other