7P8R

X-ray structure of the adduct of a vanadium picolinate complex with RNase A at pH 5.1

Summary for 7P8R

• Entry DOI: 10.2210/pdb7p8r/pdb
• Descriptor: Ribonuclease pancreatic, hydroxy(oxo)bis(pyridine-2-carboxylato-kappa~2~N,O)vanadium(3+), SULFATE ION, ... (4 entities in total)
• Functional Keywords: vanadium, ribonuclease, metalation, rna binding protein
• Biological source: Bos taurus (cattle)
• Total number of polymer chains: 2
• Total formula weight: 27936.93

Authors

Ferraro, G.,Merlino, A. (deposition date: 2021-07-23, release date: 2021-12-22, Last modification date: 2024-11-13)

Primary citation

Ferraro, G.,Demitri, N.,Vitale, L.,Sciortino, G.,Sanna, D.,Ugone, V.,Garribba, E.,Merlino, A.
Spectroscopic/Computational Characterization and the X-ray Structure of the Adduct of the V IV O-Picolinato Complex with RNase A.
Inorg.Chem., 60:19098-19109, 2021

PubMed Abstract: The structure, stability, and enzymatic activity of the adduct formed upon the reaction of the V-picolinato (pic) complex [VO(pic)(HO)], with an octahedral geometry and the water ligand in to the V═O group, with the bovine pancreatic ribonuclease (RNase A) were studied. While electrospray ionization-mass spectrometry, circular dichroism, and ultraviolet-visible absorption spectroscopy substantiate the interaction between the metal moiety and RNase A, electron paramagnetic resonance (EPR) allows us to determine that a carboxylate group, stemming from Asp or Glu residues, and imidazole nitrogen from His residues are involved in the V binding at acidic and physiological pH, respectively. Crystallographic data demonstrate that the VO(pic) moiety coordinates the side chain of Glu111 of RNase A, by substituting the equatorial water molecule at acidic pH. Computational methods confirm that Glu111 is the most affine residue and interacts favorably with the -6-23-Δ enantiomer establishing an extended network of hydrogen bonds and van der Waals stabilizations. By increasing the pH around neutrality, with the deprotonation of histidine side chains, the binding of the V complex to His105 and His119 could occur, with that to His105 which should be preferred when compared to that to the catalytically important His119. The binding of the V compound affects the enzymatic activity of RNase A, but it does not alter its overall structure and stability.

PubMed: 34847328
DOI: 10.1021/acs.inorgchem.1c02912

Experimental method

X-RAY DIFFRACTION (1.27 Å)