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PDBsum entry 1z6s

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1z6s
Jmol
Contents
Protein chains
124 a.a. *
Ligands
AMP ×2
Waters ×330
* Residue conservation analysis
PDB id:
1z6s
Name: Hydrolase
Title: Ribonuclease a- amp complex
Structure: Ribonuclease pancreatic. Chain: a, b. Synonym: ribonuclease a, rnase a, rnase 1. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
1.50Å     R-factor:   0.195     R-free:   0.231
Authors: G.N.Hatzopoulos,D.D.Leonidas,R.Kardakaris,J.Kobe,N.G.Oikonom
Key ref:
G.N.Hatzopoulos et al. (2005). The binding of IMP to ribonuclease A. FEBS J, 272, 3988-4001. PubMed id: 16045769 DOI: 10.1111/j.1742-4658.2005.04822.x
Date:
23-Mar-05     Release date:   16-Aug-05    
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: 10.1111/j.1742-4658.2005.04822.x FEBS J 272:3988-4001 (2005)
PubMed id: 16045769  
 
 
The binding of IMP to ribonuclease A.
G.N.Hatzopoulos, D.D.Leonidas, R.Kardakaris, J.Kobe, N.G.Oikonomakos.
 
  ABSTRACT  
 
The binding of inosine 5' phosphate (IMP) to ribonuclease A has been studied by kinetic and X-ray crystallographic experiments at high (1.5 A) resolution. IMP is a competitive inhibitor of the enzyme with respect to C>p and binds to the catalytic cleft by anchoring three IMP molecules in a novel binding mode. The three IMP molecules are connected to each other by hydrogen bond and van der Waals interactions and collectively occupy the B1R1P1B2P0P(-1) region of the ribonucleolytic active site. One of the IMP molecules binds with its nucleobase in the outskirts of the B2 subsite and interacts with Glu111 while its phosphoryl group binds in P1. Another IMP molecule binds by following the retro-binding mode previously observed only for guanosines with its nucleobase at B1 and the phosphoryl group in P(-1). The third IMP molecule binds in a novel mode towards the C-terminus. The RNase A-IMP complex provides structural evidence for the functional components of subsite P(-1) while it further supports the role inferred by other studies to Asn71 as the primary structural determinant for the adenine specificity of the B2 subsite. Comparative structural analysis of the IMP and AMP complexes highlights key aspects of the specificity of the base binding subsites of RNase A and provides a structural explanation for their potencies. The binding of IMP suggests ways to develop more potent inhibitors of the pancreatic RNase superfamily using this nucleotide as the starting point.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereodiagrams of the interactions between RNase A and IMP molecules I (A), II (B), and III (C) in the active site. The side chains of protein residues involved in ligand binding are shown as ball-and-stick models. Bound water molecules are shown as black spheres. Hydrogen bond interactions are represented in dashed lines.
Figure 4.
Fig. 4. Stereodiagrams of the interactions of AMP in the RNase A active site. The side chains of protein residues involved in ligand binding are shown as ball-and-stick models. Bound waters are shown as black spheres. Hydrogen bond interactions are represented in dashed lines.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2005, 272, 3988-4001) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20522942 K.Rlepokura, and R.Petrus (2010).
Nucleotide-amino acid interactions in the L-His-IMP.MeOH.H(2)O complex.
  Acta Crystallogr C, 66, o265-o269.  
  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
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
  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
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 code is shown on the right.