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PDBsum entry 3dic

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protein ligands metals links
Hydrolase PDB id
3dic
Jmol
Contents
Protein chain
124 a.a. *
Ligands
SO4
Metals
_CL ×3
Waters ×210
* Residue conservation analysis
PDB id:
3dic
Name: Hydrolase
Title: Crystal structure of bovine pancreatic ribonuclease a variant (v108a)
Structure: Ribonuclease pancreatic. Chain: a. Synonym: pancreatic ribonuclease a, rnase 1, rnase a. Engineered: yes. Mutation: yes
Source: Bos taurus. Bovine. Organism_taxid: 9913. Gene: rnase1, rns1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.60Å     R-factor:   0.188     R-free:   0.210
Authors: K.Kurpiewska,J.Font,M.Ribo,M.Vilanova,K.Lewinski
Key ref:
K.Kurpiewska et al. (2009). X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability. Proteins, 77, 658-669. PubMed id: 19544568 DOI: 10.1002/prot.22480
Date:
20-Jun-08     Release date:   15-Jul-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1002/prot.22480 Proteins 77:658-669 (2009)
PubMed id: 19544568  
 
 
X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability.
K.Kurpiewska, J.Font, M.Ribó, M.Vilanova, K.LewiƄski.
 
  ABSTRACT  
 
To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Secondary structure of RNase A with depicting the mutation region, site chains of mutated amino acids are indicated as sticks representation. The picture was generated using the program PyMol[66].
Figure 3.
Figure 3. Main cavity formed inside the hydrophobic core of mutated structures of RNase A differs in size and shape and depends on the localization of introduced mutation: wt(A), V47A (B), V54A (C), V57A (D), I81A (E), I106A (F), and V108A (G).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 77, 658-669) copyright 2009.  
  Figures were selected by an automated process.