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PDBsum entry 1jn4

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1jn4
Jmol
Contents
Protein chains
124 a.a. *
Ligands
139
Waters ×265
* Residue conservation analysis
PDB id:
1jn4
Name: Hydrolase
Title: The crystal structure of ribonuclease a in complex with 2'- deoxyuridine 3'-pyrophosphate (p'-5') adenosine
Structure: Pancreatic ribonuclease a. Chain: a, b. Synonym: rnase 1. Rnase a. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pankreas
Resolution:
1.80Å     R-factor:   0.225     R-free:   0.295
Authors: A.M.Jardine,D.D.Leonidas,J.L.Jenkins,C.Park,R.T.Raines, K.R.Acharya,R.Shapiro
Key ref:
A.M.Jardine et al. (2001). Cleavage of 3',5'-pyrophosphate-linked dinucleotides by ribonuclease A and angiogenin. Biochemistry, 40, 10262-10272. PubMed id: 11513604 DOI: 10.1021/bi010888j
Date:
23-Jul-01     Release date:   03-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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: 10.1021/bi010888j Biochemistry 40:10262-10272 (2001)
PubMed id: 11513604  
 
 
Cleavage of 3',5'-pyrophosphate-linked dinucleotides by ribonuclease A and angiogenin.
A.M.Jardine, D.D.Leonidas, J.L.Jenkins, C.Park, R.T.Raines, K.R.Acharya, R.Shapiro.
 
  ABSTRACT  
 
Recently, 3',5'-pyrophosphate-linked 2'-deoxyribodinucleotides were shown to be >100-fold more effective inhibitors of RNase A superfamily enzymes than were the corresponding monophosphate-linked (i.e., standard) dinucleotides. Here, we have investigated two ribo analogues of these compounds, cytidine 3'-pyrophosphate (P'-->5') adenosine (CppA) and uridine 3'-pyrophosphate (P'-->5') adenosine (UppA), as potential substrates for RNase A and angiogenin. CppA and UppA are cleaved efficiently by RNase A, yielding as products 5'-AMP and cytidine or uridine cyclic 2',3'-phosphate. The k(cat)/K(m) values are only 4-fold smaller than for the standard dinucleotides CpA and UpA, and the K(m) values (10-16 microM) are lower than those reported for any earlier small substrates (e.g., 500-700 microM for CpA and UpA). The k(cat)/K(m) value for CppA with angiogenin is also only severalfold smaller than for CpA, but the effect of lengthening the internucleotide linkage on K(m) is more modest. Ribonucleotide 3',5'-pyrophosphate linkages were proposed previously to exist in nature as chemically labile intermediates in the pathway for the generation of cyclic 2',3'-phosphate termini in various RNAs. We demonstrate that in fact they are relatively stable (t(1/2) > 15 days for uncatalyzed degradation of UppA at pH 6 and 25 degrees C) and that cleavage in vivo is most likely enzymatic. Replacements of the RNase A catalytic residues His12 and His119 by alanine reduce activity toward UppA by approximately 10(5)-and 10(3.3)-fold, respectively. Thus, both residues play important roles. His12 probably acts as a base catalyst in cleavage of UppA (as with RNA). However, the major function of His119 in RNA cleavage, protonation of the 5'-O leaving group, is not required for UppA cleavage because the pK(a) of the leaving group is much lower than that for RNA substrates. A crystal structure of the complex of RNase A with 2'-deoxyuridine 3'-pyrophosphate (P'-->5') adenosine (dUppA), determined at 1.7 A resolution, together with models of the UppA complex based on this structure suggest that His119 contributes to UppA cleavage through a hydrogen bond with a nonbridging oxygen atom in the pyrophosphate and through pi-pi stacking with the six-membered ring of adenine.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19191310 D.E.Holloway, G.B.Chavali, D.D.Leonidas, M.D.Baker, and K.R.Acharya (2009).
Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: An X-ray crystallographic study.
  Biopolymers, 91, 995.
PDB codes: 2w5g 2w5i 2w5k 2w5l 2w5m
19452557 M.Amitay, and A.Shurki (2009).
The structure of G117H mutant of butyrylcholinesterase: nerve agents scavenger.
  Proteins, 77, 370-377.  
  17768339 S.B.Larson, J.S.Day, R.Cudney, and A.McPherson (2007).
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 728-733.
PDB code: 2qca
17142283 S.Polydoridis, D.D.Leonidas, N.G.Oikonomakos, and G.Archontis (2007).
Recognition of ribonuclease a by 3'-5'-pyrophosphate-linked dinucleotide inhibitors: a molecular dynamics/continuum electrostatics analysis.
  Biophys J, 92, 1659-1672.  
16730994 D.D.Leonidas, T.K.Maiti, A.Samanta, S.Dasgupta, T.Pathak, S.E.Zographos, and N.G.Oikonomakos (2006).
The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.
  Bioorg Med Chem, 14, 6055-6064.
PDB codes: 2g8q 2g8r
16045769 G.N.Hatzopoulos, D.D.Leonidas, R.Kardakaris, J.Kobe, and N.G.Oikonomakos (2005).
The binding of IMP to ribonuclease A.
  FEBS J, 272, 3988-4001.
PDB codes: 1z6d 1z6s
14573867 D.D.Leonidas, G.B.Chavali, N.G.Oikonomakos, E.D.Chrysina, M.N.Kosmopoulou, M.Vlassi, C.Frankling, and K.R.Acharya (2003).
High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.
  Protein Sci, 12, 2559-2574.
PDB codes: 1o0f 1o0h 1o0m 1o0n 1o0o
12833549 F.Sica, A.Di Fiore, A.Zagari, and L.Mazzarella (2003).
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative.
  Proteins, 52, 263-271.
PDB codes: 1n1x 1n3z
12118120 R.Y.Kao, J.L.Jenkins, K.A.Olson, M.E.Key, J.W.Fett, and R.Shapiro (2002).
A small-molecule inhibitor of the ribonucleolytic activity of human angiogenin that possesses antitumor activity.
  Proc Natl Acad Sci U S A, 99, 10066-10071.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.