PDBsum entry 1kh8

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Hydrolase PDB id
Protein chain
125 a.a. *
Waters ×62
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of a cis-proline (p114) to glycine variant of ribonuclease a
Structure: Pancreatic ribonuclease a. Chain: a. Synonym: ribonuclease pancreatic, rnase 1, rnase a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562
2.00Å     R-factor:   0.195     R-free:   0.219
Authors: D.A.Schultz,A.M.Friedman,M.A.White,R.O.Fox
Key ref:
D.A.Schultz et al. (2005). The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A. Protein Sci, 14, 2862-2870. PubMed id: 16199662 DOI: 10.1110/ps.051610505
29-Nov-01     Release date:   17-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
125 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1110/ps.051610505 Protein Sci 14:2862-2870 (2005)
PubMed id: 16199662  
The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A.
D.A.Schultz, A.M.Friedman, M.A.White, R.O.Fox.
Replacement of a cis-proline by glycine at position 114 in ribonuclease A leads to a large decrease in thermal stability and simplifies the refolding kinetics. A crystallographic approach was used to determine whether the decrease in thermal stability results from the presence of a cis glycine peptide bond, or from a localized structural rearrangement caused by the isomerization of the mutated cis 114 peptide bond. The structure was solved at 2.0 A resolution and refined to an R-factor of 19.5% and an R(free) of 21.9%. The overall conformation of the protein was similar to that of wild-type ribonuclease A; however, there was a large localized rearrangement of the mutated loop (residues 110-117-a 9.3 A shift of the Calpha atom of residue 114). The peptide bond before Gly114 is in the trans configuration. Interestingly, a large anomalous difference density was found near residue 114, and was attributed to a bound cesium ion present in the crystallization experiment. The trans isomeric configuration of the peptide bond in the folded state of this mutant is consistent with the refolding kinetics previously reported, and the associated protein conformational change provides an explanation for the decreased thermal stability.
  Selected figure(s)  
Figure 1.
Figure 1. Electron density surrounding the site of the P114G substitution, with coordinates from the final refined structure. The configuration of the peptide bond preceding the mutated residue 114 is now trans. The fit of the carbonyl groups for residues 113 and 114 to the density confirms the trans configuration. The density corresponding to the bound cesium ion is also easily observed. Nitrogen, carbon, oxygen, and amide hydrogen atoms are colored blue, gray, red, and white, respectively.
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2005, 14, 2862-2870) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20977676 J.Tian, P.Wang, S.Gao, X.Chu, N.Wu, and Y.Fan (2010).
Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation.
  FEBS J, 277, 4901-4908.  
19706593 D.A.Gell, L.Feng, S.Zhou, P.D.Jeffrey, K.Bendak, A.Gow, M.J.Weiss, Y.Shi, and J.P.Mackay (2009).
A cis-proline in alpha-hemoglobin stabilizing protein directs the structural reorganization of alpha-hemoglobin.
  J Biol Chem, 284, 29462-29469.
PDB code: 3ia3
19018102 L.C.Tsai, H.C.Huang, C.H.Hsiao, Y.N.Chiang, L.F.Shyur, Y.S.Lin, and S.H.Lee (2008).
Mutational and structural studies of the active-site residues in truncated Fibrobacter succinogenes1,3-1,4-beta-D-glucanase.
  Acta Crystallogr D Biol Crystallogr, 64, 1259-1266.  
16600965 G.E.Gómez, A.Cauerhff, P.O.Craig, F.A.Goldbaum, and J.M.Delfino (2006).
Exploring protein interfaces with a general photochemical reagent.
  Protein Sci, 15, 744-752.  
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