PDBsum entry 1rta

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protein dna_rna links
Hydrolase/DNA PDB id
Protein chain
124 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease a
Structure: DNA (5'-d( Tp Tp Tp T)-3'). Chain: c. Engineered: yes. Protein (ribonuclease a . Chain: e. Ec:
Source: Synthetic: yes. Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Secretion: milk
2.50Å     R-factor:   0.235    
Authors: D.L.Birdsall,A.Mcpherson
Key ref: D.L.Birdsall and A.McPherson (1992). Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A. J Biol Chem, 267, 22230-22236. PubMed id: 1429575
28-Aug-92     Release date:   31-Oct-93    
Go to PROCHECK summary

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     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     6 terms  


J Biol Chem 267:22230-22236 (1992)
PubMed id: 1429575  
Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A.
D.L.Birdsall, A.McPherson.
The crystal structure of ribonuclease A with bound thymidylic acid tetramer is reported at 2.5-A resolution. The diffusion of the tetramer into native orthorhombic crystals of the ribonuclease allows for the formation of a structurally stable complex where the single-stranded nucleic acid enters and leaves the enzyme's catalytic region in a persistent 5'-3' direction. The binding of the tetramer to the enzyme's surface is facilitated and mediated by electrostatic interactions between basic protein residues and nucleotide phosphates. Two pyrimidine nucleotides are bound to the enzyme's active site in a manner similar to that observed for other complexes between ribonuclease A and nucleic acid oligomers.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20124705 S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, and A.McPherson (2010).
Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 113-120.
PDB code: 3jw1
20301119 S.Ganguli, K.Yoshimoto, S.Tomita, H.Sakuma, T.Matsuoka, K.Shiraki, and Y.Nagasaki (2010).
Improving the heat resistance of ribonuclease A by the addition of poly(N,N-diethylaminoethyl methacrylate)-graft-poly(ethylene glycol) (PEAMA-g-PEG).
  Macromol Biosci, 10, 853-859.  
15273275 N.G.Beloglazova, M.M.Fabani, M.A.Zenkova, E.V.Bichenkova, N.N.Polushin, V.V.Sil'nikov, K.T.Douglas, and V.V.Vlassov (2004).
Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy.
  Nucleic Acids Res, 32, 3887-3897.  
11790847 Y.Liu, G.Gotte, M.Libonati, and D.Eisenberg (2002).
Structures of the two 3D domain-swapped RNase A trimers.
  Protein Sci, 11, 371-380.
PDB code: 1js0
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
9520384 Y.Liu, P.J.Hart, M.P.Schlunegger, and D.Eisenberg (1998).
The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution.
  Proc Natl Acad Sci U S A, 95, 3437-3442.
PDB code: 1a2w
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