1CB9

NMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II (CARDIOTOXIN) FROM NAJA NAJA OXIANA IN AQUEOUS SOLUTION (MAJOR FORM).

Summary for 1CB9

• Entry DOI: 10.2210/pdb1cb9/pdb
• NMR Information: BMRB: 4419
• Descriptor: PROTEIN (CYTOTOXIN 2) (2 entities in total)
• Functional Keywords: cytoxin (cardiotoxin), membrane perturbation, cis/trans isomerization, bound water, toxin
• Biological source: Naja oxiana (Central Asian cobra)
• Cellular location: Secreted : P01441
• Total number of polymer chains: 1
• Total formula weight: 6648.24

Authors

Dementieva, D.V.,Bocharov, E.V.,Arseniev, A.S. (deposition date: 1999-03-01, release date: 1999-06-29, Last modification date: 2024-10-30)

Primary citation

Dementieva, D.V.,Bocharov, E.V.,Arseniev, A.S.
Two forms of cytotoxin II (cardiotoxin) from Naja naja oxiana in aqueous solution: spatial structures with tightly bound water molecules.
Eur.J.Biochem., 263:152-162, 1999

PubMed Abstract: 1H-NMR spectroscopy data, such as NOE intraprotein and (bound water)/protein contacts, 3J coupling constants and deuterium exchange rates were used to determine the in-solution spatial structure of cytotoxin II from Naja naja oxiana snake venom (CTII). Exploiting information from two 1H-NMR spectral components, shown to be due to cis/trans isomerization of the Val7-Pro8 peptide bond, spatial structures of CTII minor and major forms (1 : 6) were calculated using the torsion angle dynamics algorithm of the DYANA program and then energy refined using the FANTOM program. Each form, major and minor, is represented by 20 resulting conformers, demonstrating mean backbone rmsd values of 0.51 and 0.71 A, respectively. Two forms of CTII preserve the structural skeleton as three large loops, including two beta-sheets with bend regions, and demonstrate structural differences at loop I, where cis/trans isomerization occurs. The CTII side-chain distribution constitutes hydrophilic and hydrophobic belts around the protein, alternating in the trend of the three main loops. Because of the Omega-shaped backbone, formed in participation with two bound water molecules, the tip of loop II bridges the tips of loops I and III. This ensures the continuity of the largest hydrophobic belt, formed with the residues of these tips. Comparison revealed pronounced differences in the spatial organization of the tips of the three main loops between CTII and previous structures of homologous cytotoxins (cardiotoxins) in solution.

PubMed: 10429199
DOI: 10.1046/j.1432-1327.1999.00478.x

Experimental method

SOLUTION NMR