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PDBsum entry 1rnq

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Hydrolase (phosphoric diester) PDB id
1rnq
Jmol
Contents
Protein chain
124 a.a. *
Ligands
FMT ×2
Waters ×89
* Residue conservation analysis
PDB id:
1rnq
Name: Hydrolase (phosphoric diester)
Title: Ribonuclease a crystallized from 8m sodium formate
Structure: Ribonuclease a. Chain: a. Synonym: rnase a. Other_details: crystallized from 8m sodium formate
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.161    
Authors: A.A.Fedorov,D.Josef-Mccarthy,I.Graf,D.Anguelova,E.V.Fedorov, S.C.Almo
Key ref:
A.A.Fedorov et al. (1996). Ionic interactions in crystalline bovine pancreatic ribonuclease A. Biochemistry, 35, 15962-15979. PubMed id: 8973167 DOI: 10.1021/bi961533g
Date:
08-Nov-95     Release date:   03-Apr-96    
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: 10.1021/bi961533g Biochemistry 35:15962-15979 (1996)
PubMed id: 8973167  
 
 
Ionic interactions in crystalline bovine pancreatic ribonuclease A.
A.A.Fedorov, D.Joseph-McCarthy, E.Fedorov, D.Sirakova, I.Graf, S.C.Almo.
 
  ABSTRACT  
 
Isomorphous crystals (space group P3(2)21) of bovine pancreatic ribonuclease A (RNase A) were prepared at a pH of 5.5 in a series of high salt conditions, where both the nature of the ions and the ionic strength varied: 80% ammonium sulfate (mu = 12.5); 8 M sodium formate (mu = 8.0); 3 M NaCl, 30% ammonium sulfate (mu = 7.0); 3 M CsCl, 30% ammonium sulfate (mu = 7.0); and 2.5 M NaCl, 3.3 M sodium formate (mu = 5.8). These structures were independently refined to a resolution of 2.0 A or better with R-factors that range from 16.1% to 17.5%. A comparison of these six structures and the monoclinic crystal form of RNase A grown from alcohol shows that changes in ionic strength do not alter the secondary or tertiary structure and that there are no significant changes in intramolecular salt bridges. These findings support the notion that structures determined from crystals grown in high salt are representative of the overall structural and electrostatic features present under physiological conditions. While little effect was observed on the main chain conformation, several residues adopted different side chain conformations and altered hydrogen-bonding patterns, either as result of direct anion binding or more subtle indirect effects. Changes in the ionic composition of the mother liquor allowed for the occupancy of the active site with different anions. The direct observation of active site-bound chloride and formate anions supports the proposal that these species act as true competitive inhibitors of RNase A and not through nonspecific electrostatic effects. The identification of bound formate anions allowed for an experimental validation of computational-based functional group mapping techniques and suggests a useful modification to these approaches. Electrostatic surface potential calculations identify a nearly continuous band of positive potential, consistent with an extended binding site for polynucleotide ligands and substrates. The majority of these residues are not involved in salt bridges, which may facilitate binding to extended polynucleotide substrates. Selection of the appropriate solvent conditions results in an unoccupied active site, which will allow this crystal form to be used for the crystallographic study of productive ligand-binding modes.
 

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
18508078 K.Kazakou, D.E.Holloway, S.H.Prior, V.Subramanian, and K.R.Acharya (2008).
Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications.
  J Mol Biol, 380, 206-222.
PDB codes: 2vq8 2vq9
17044066 B.L.Simons, H.Kaplan, S.M.Fournier, T.Cyr, and M.A.Hefford (2007).
A novel cross-linked RNase A dimer with enhanced enzymatic properties.
  Proteins, 66, 183-195.  
  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
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
16791739 N.Powers, and J.H.Jensen (2006).
Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.
  J Biomol NMR, 35, 39-51.  
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
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
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.  
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
12486724 P.M.Tessier, H.R.Johnson, R.Pazhianur, B.W.Berger, J.L.Prentice, B.J.Bahnson, S.I.Sandler, and A.M.Lenhoff (2003).
Predictive crystallization of ribonuclease A via rapid screening of osmotic second virial coefficients.
  Proteins, 50, 303-311.  
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.  
11742124 E.Chatani, R.Hayashi, H.Moriyama, and T.Ueki (2002).
Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 A resolution.
  Protein Sci, 11, 72-81.
PDB codes: 1eic 1eid 1eie 1fs3
11876642 G.J.Swaminathan, D.E.Holloway, K.Veluraja, and K.R.Acharya (2002).
Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.
  Biochemistry, 41, 3341-3352.
PDB code: 1gqv
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
11087402 B.R.Kelemen, L.W.Schultz, R.Y.Sweeney, and R.T.Raines (2000).
Excavating an active site: the nucleobase specificity of ribonuclease A.
  Biochemistry, 39, 14487-14494.
PDB code: 1c8w
10665832 G.K.Farber (1999).
New approaches to rational drug design.
  Pharmacol Ther, 84, 327-332.  
10500299 J.R.Tame (1999).
What is the true structure of liganded haemoglobin?
  Trends Biochem Sci, 24, 372-377.  
9860854 B.M.Fisher, L.W.Schultz, and R.T.Raines (1998).
Coulombic effects of remote subsites on the active site of ribonuclease A.
  Biochemistry, 37, 17386-17401.
PDB codes: 3rsk 4rsk
9801446 J.Chopineau, S.Robert, L.Fénart, R.Cecchelli, B.Lagoutte, S.Paitier, M.P.Dehouck, and D.Domurado (1998).
Monoacylation of ribonuclease A enables its transport across an in vitro model of the blood-brain barrier.
  J Control Release, 56, 231-237.  
9636030 L.W.Schultz, D.J.Quirk, and R.T.Raines (1998).
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
  Biochemistry, 37, 8886-8898.
PDB codes: 3rsd 4rsd
  9684895 L.W.Schultz, S.R.Hargraves, T.A.Klink, and R.T.Raines (1998).
Structure and stability of the P93G variant of ribonuclease A.
  Protein Sci, 7, 1620-1625.
PDB code: 3rsp
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.