PDBsum entry 3ev3

Hydrolase

PDB id: 3ev3

Contents

Protein chains

121 a.a. *

Ligands

TBU

Waters ×320

* Residue conservation analysis

PDB id:

3ev3

Name:

Hydrolase

Title:

Crystal structure of ribonuclease a in 70% t-butanol

Structure:

Ribonuclease pancreatic. Chain: a, b. Synonym: rnase 1, rnase a. Ec: 3.1.27.5

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Organ: pancreas

Resolution:

1.68Å R-factor: 0.207 R-free: 0.233

Authors:

M.Dechene,G.Wink,M.Smith,P.Swartz,C.Mattos

Key ref:

M.Dechene et al. (2009). Multiple solvent crystal structures of ribonuclease A: An assessment of the method. Proteins, 76, 861-881. PubMed id: 19291738 DOI: 10.1002/prot.22393

Date:

12-Oct-08 Release date: 23-Jun-09

Protein chains

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic from Bos taurus

Seq: 150 a.a.

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: E.C.4.6.1.18 - pancreatic ribonuclease.
• Reaction:
  1. an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
  2. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]

DOI no: 10.1002/prot.22393

Proteins 76:861-881 (2009)

PubMed id: 19291738

Multiple solvent crystal structures of ribonuclease A: An assessment of the method.

M.Dechene, G.Wink, M.Smith, P.Swartz, C.Mattos.

ABSTRACT

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS. Proteins 2009. (c) 2009 Wiley-Liss, Inc.

Selected figure(s)

Figure 3.
Figure 3. Crystallographic water molecules on the surface of RNAse A shown as red spheres. Water molecules from one representative MSCS model are shown on the left. Water molecules superimposed from all 20 MSCS models are shown on the right. This figure was prepared using Pymol (Delano Scientific).

Figure 6.
Figure 6. Organic solvent binding sites on the surface of RNAse A. Ribbon diagram of RNAse A showing the binding sites for organic solvent molecules. The -strands are shown in dark gray and the -helices are shown in purple. Residues 16-22 are colored in salmon. The organic solvent molecules are colored as follows: DIO, red; DMF, purple; DMS, green; HEZ, orange; IPA, blue; RSF, yellow; TBU, cyan; ETF, brown; and TMO, black. Organic solvent binding sites are numbered as in Supporting Information Table sII. The RNAse active site pockets are labeled. This figure was prepared using Pymol (Delano Scientific).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 76, 861-881) copyright 2009.

Figures were selected by an automated process.