1U1B

Structure of bovine pancreatic Ribonuclease A in complex with 3'-phosphothymidine (3'-5')-pyrophosphate adenosine 3'-phosphate

Summary for 1U1B

• Entry DOI: 10.2210/pdb1u1b/pdb
• Related: 1QHC
• Descriptor: Ribonuclease, pancreatic, 5'-PHOSPHOTHYMIDINE (3'-5')-PYROPHOSPHATE ADENOSINE 3'-PHOSPHATE (3 entities in total)
• Functional Keywords: hydrolase, ribonuclease, endonuclease, nucleotide inhibitor
• Biological source: Bos taurus (cattle)
• Cellular location: Secreted: P61823
• Total number of polymer chains: 2
• Total formula weight: 29035.37

Authors

Beach, H.,Cole, R.,Gill, M.L.,Loria, J.P. (deposition date: 2004-07-15, release date: 2005-06-28, Last modification date: 2024-10-30)

Primary citation

Beach, H.,Cole, R.,Gill, M.L.,Loria, J.P.
Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state.
J.Am.Chem.Soc., 127:9167-9176, 2005

PubMed Abstract: Solution NMR spin-relaxation experiments were used to compare mus-ms dynamics in RNase A in the apo form and as complexed to the substrate-mimic, pTppAp. The crystal structure of the RNase A/pTppAp complex was determined and demonstrates that this ligand binds at the active site and utilizes established substrate binding sites in its interaction with RNase A. Relaxation-compensated CPMG experiments identify flexible residues in and around the active site in both the apo and pTppAp-bound enzyme. Quantitative analysis of the NMR spin-relaxation dispersion curves show that the time scale of motion in RNase A is unchanged when pTppAp binds and is similar to the time scale for the rate-determining step of the catalytic reaction. Temperature-dependent measurements provide an activation barrier for motion of 5.2 +/- 1.0 kcal/mol and 4.5 +/- 1.2 kcal/mol for the apo and pTppAp forms of RNase A, respectively. These data indicate very similar motion exists in the free and bound enzyme. Additionally, chemical shift data suggests that the magnitude of motion is also similar for these two forms and that it is likely that apo enzyme interconverts to a structure that resembles a ligand-bound form. Likewise, it appears that the bound conformation samples the apo enzyme form even when ligand is present. Taken together the data imply that RNase A is in a preexisting dynamic equilibrium between two conformations that represent the open and closed enzyme forms. These data suggest that ligand binding stabilizes the bound conformer but does not induce it.

PubMed: 15969595
DOI: 10.1021/ja0514949

Experimental method

X-RAY DIFFRACTION (2 Å)