PDBsum entry 3lxo

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protein ligands links
Hydrolase PDB id
Jmol PyMol
Protein chain
124 a.a. *
Waters ×129
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: The crystal structure of ribonuclease a in complex with thym monophosphate
Structure: Ribonuclease pancreatic. Chain: a. Synonym: rnase 1, rnase a. Ec:
Source: Bos taurus. Bovine,cow,domestic cattle,domestic cow. Organism_taxid: 9913. Other_details: pancreas
1.55Å     R-factor:   0.145     R-free:   0.181
Authors: N.Doucet,T.B.Jayasundera,M.Simonovic,J.P.Loria
Key ref: N.Doucet et al. (2010). The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding. Proteins, 78, 2459-2468. PubMed id: 20602460
25-Feb-10     Release date:   28-Apr-10    
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Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     nucleic acid binding     7 terms  


Proteins 78:2459-2468 (2010)
PubMed id: 20602460  
The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding.
N.Doucet, T.B.Jayasundera, M.Simonović, J.P.Loria.
Thymidine-3'-monophosphate (3'-TMP) is a competitive inhibitor analogue of the 3'-CMP and 3'-UMP natural product inhibitors of bovine pancreatic ribonuclease A (RNase A). Isothermal titration calorimetry experiments show that 3'-TMP binds the enzyme with a dissociation constant (K(d)) of 15 muM making it one of the strongest binding members of the five natural bases found in nucleic acids (A, C, G, T, and U). To further investigate the molecular properties of this potent natural affinity, we have determined the crystal structure of bovine pancreatic RNase A in complex with 3'-TMP at 1.55 A resolution and we have performed NMR binding experiments with 3'-CMP and 3'-TMP. Our results show that binding of 3'-TMP is very similar to other natural and non-natural pyrimidine ligands, demonstrating that single nucleotide affinity is independent of the presence or absence of a 2'-hydroxyl on the ribose moiety of pyrimidines and suggesting that the pyrimidine binding subsite of RNase A is not a significant contributor of inhibitor discrimination. Accumulating evidence suggests that very subtle structural, chemical, and potentially motional variations contribute to ligand discrimination in this enzyme. Proteins 2010. (c) 2010 Wiley-Liss, Inc.