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PDBsum entry 1eow

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protein ligands links
Hydrolase PDB id
1eow
Jmol
Contents
Protein chain
124 a.a. *
Ligands
SO4
U2G
Waters ×72
* Residue conservation analysis
PDB id:
1eow
Name: Hydrolase
Title: Crystal structure of ribonuclease a complexed with uridylyl(2',5')guanosine (non-productive binding)
Structure: Ribonuclease pancreatic. Chain: a. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
2.00Å     R-factor:   0.187    
Authors: L.Vitagliano,A.Merlino,A.Zagari,L.Mazzarella
Key ref: L.Vitagliano et al. (2000). Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine. Protein Sci, 9, 1217-1225. PubMed id: 10892814 DOI: 10.1110/ps.9.6.1217
Date:
24-Mar-00     Release date:   17-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
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: 10.1110/ps.9.6.1217 Protein Sci 9:1217-1225 (2000)
PubMed id: 10892814  
 
 
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.
L.Vitagliano, A.Merlino, A.Zagari, L.Mazzarella.
 
  ABSTRACT  
 
Guanine-containing mono- and dinucleotides bind to the active site of ribonuclease A in a nonproductive mode (retro-binding) (Aguilar CF, Thomas PJ, Mills A, Moss DS, Palmer RA. 1992. J Mol Biol 224:265-267). Guanine binds to the highly specific pyrimidine site by forming hydrogen bonds with Thr45 and with the sulfate anion located in the P1 site. To investigate the influence of the anion present in the P1 site on retro-binding, we determined the structure of two new complexes of RNase A with uridylyl(2',5')guanosine obtained by soaking two different forms of pre-grown RNase A crystals. In one case, RNase A was crystallized without removing the sulfate anion strongly bound to the active site; in the other, the protein was first equilibrated with a basic solution to displace the anion from the P1 site. The X-ray structures of the complexes with and without sulfate in P1 were refined using diffraction data up to 1.8 A (R-factor 0.192) and 2.0 A (R-factor 0.178), respectively. The binding mode of the substrate analogue to the protein differs markedly in the two complexes. When the sulfate is located in P1, we observe retro-binding; whereas when the anion is removed from the active site, the uridine is productively bound at the B1 site. In the productive complex, the electron density is very well defined for the uridine moiety, whereas the downstream guanine is disordered. This finding indicates that the interactions of guanine in the B2 site are rather weak and that this site is essentially adenine preferring. In this crystal form, there are two molecules per asymmetric unit, and due to crystal packing, only the active site of one molecule is accessible to the ligand. Thus, in the same crystal we have a ligand-bound and a ligand-free RNase A molecule. The comparison of these two structures furnishes a detailed and reliable picture of the structural alterations induced by the binding of the substrate. These results provide structural information to support the hypotheses on the role of RNase A active site residues that have recently emerged from site-directed mutagenesis studies.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205197 N.Thiyagarajan, B.D.Smith, R.T.Raines, and K.R.Acharya (2011).
Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A.
  FEBS J, 278, 541-549.
PDB codes: 2xog 2xoi
21050179 E.Pizzo, A.Merlino, M.Turano, I.Russo Krauss, F.Coscia, A.Zanfardino, M.Varcamonti, A.Furia, C.Giancola, L.Mazzarella, F.Sica, and G.D'Alessio (2010).
A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.
  Biochem J, 433, 345-355.
PDB codes: 3ljd 3lje 3ln8
19280639 A.Merlino, I.Russo Krauss, M.Perillo, C.A.Mattia, C.Ercole, D.Picone, A.Vergara, and F.Sica (2009).
Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants.
  Biopolymers, 91, 1029-1037.
PDB codes: 3fkz 3fl0 3fl1 3fl3
18423397 A.T.Torelli, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2008).
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
  Biochem Biophys Res Commun, 371, 154-158.
PDB code: 3cqs
  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
16862454 A.A.Moosavi-Movahedi, M.Gharanfoli, S.Jalili, F.Ahmad, J.Chamani, G.H.Hakimelahi, M.Sadeghi, M.Amani, and A.A.Saboury (2006).
The correlation of RNase A enzymatic activity with the changes in the distance between Nepsilon2-His12 and N delta1-His119 upon addition of stabilizing and destabilizing salts.
  Protein J, 25, 117-125.  
15596505 A.Merlino, M.A.Ceruso, L.Vitagliano, and L.Mazzarella (2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
  Biophys J, 88, 2003-2012.  
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
15048772 A.Merlino, L.Vitagliano, F.Sica, A.Zagari, and L.Mazzarella (2004).
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.
  Biopolymers, 73, 689-695.
PDB codes: 1r5c 1r5d
15041676 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2004).
Dynamic properties of the N-terminal swapped dimer of ribonuclease A.
  Biophys J, 86, 2383-2391.  
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.  
12382288 A.Merlino, L.Vitagliano, M.A.Ceruso, A.Di Nola, and L.Mazzarella (2002).
Global and local motions in ribonuclease A: a molecular dynamics study.
  Biopolymers, 65, 274-283.  
11746706 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2002).
Reversible substrate-induced domain motions in ribonuclease A.
  Proteins, 46, 97.
PDB codes: 1jvt 1jvu 1jvv
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.