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PDBsum entry 1kf4

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Hydrolase PDB id
1kf4
Jmol
Contents
Protein chain
124 a.a. *
Ligands
SO4
Waters ×228
* Residue conservation analysis
PDB id:
1kf4
Name: Hydrolase
Title: Atomic resolution structure of rnase a at ph 6.3
Structure: Pancreatic ribonuclease. Chain: a. Synonym: rnase a. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.10Å     R-factor:   0.104    
Authors: R.Berisio,F.Sica,V.S.Lamzin,K.S.Wilson,A.Zagari,L.Mazzarella
Key ref:
R.Berisio et al. (2002). Atomic resolution structures of ribonuclease A at six pH values. Acta Crystallogr D Biol Crystallogr, 58, 441-450. PubMed id: 11856829 DOI: 10.1107/S0907444901021758
Date:
19-Nov-01     Release date:   19-Dec-01    
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: 10.1107/S0907444901021758 Acta Crystallogr D Biol Crystallogr 58:441-450 (2002)
PubMed id: 11856829  
 
 
Atomic resolution structures of ribonuclease A at six pH values.
R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, L.Mazzarella.
 
  ABSTRACT  
 
The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Conformational changes of the catalytic Gln11 and Lys41. (a) Superposition of the two structures at pH* 5.2 (dark grey) and 8.0 (light grey); only the most populated conformers are shown for clarity. (b) Electron-density maps (3F[o] - 2F[c]) contoured at 1.7 for the structures at pH* 5.2 and (c) at pH* 8.8. The figures were generated using the program BOBSCRIPT (Esnouf, 1999[Esnouf, R. M. (1999). Acta Cryst. D55, 938-940.]).
Figure 6.
Figure 6 Electron-density map (3F[o] - 2F[c]), contoured at 2.7 , showing the double conformation of the disulfide bridge [65-72].
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 441-450) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20208156 C.A.Nieves-Marrero, C.R.Ruiz-Martínez, R.A.Estremera-Andújar, L.A.González-Ramírez, J.López-Garriga, and J.A.Gavira (2010).
Two-step counterdiffusion protocol for the crystallization of haemoglobin II from Lucina pectinata in the pH range 4-9.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 264-268.  
  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
20583025 S.Cheng, S.A.Edwards, Y.Jiang, and F.Gräter (2010).
Glycosylation enhances peptide hydrophobic collapse by impairing solvation.
  Chemphyschem, 11, 2367-2374.  
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
18518759 A.K.Beck, H.I.Pass, M.Carbone, and H.Yang (2008).
Ranpirnase as a potential antitumor ribonuclease treatment for mesothelioma and other malignancies.
  Future Oncol, 4, 341-349.  
17937402 Y.Choi, J.H.Lee, S.Hwang, J.K.Kim, K.Jeong, and S.Jung (2008).
Retardation of the unfolding process by single N-glycosylation of ribonuclease A based on molecular dynamics simulations.
  Biopolymers, 89, 114-123.  
17612625 C.N.N'soukpoé-Kossi, C.Ragi, and H.A.Tajmir-Riahi (2007).
RNase A - tRNA binding alters protein conformation.
  Biochem Cell Biol, 85, 311-318.  
17417947 S.S.Pachouri, R.C.Sobti, P.Kaur, and J.Singh (2007).
Contrasting impact of DNA repair gene XRCC1 polymorphisms Arg399Gln and Arg194Trp on the risk of lung cancer in the north-Indian population.
  DNA Cell Biol, 26, 186-191.  
16177964 A.Torreggiani, M.Tamba, I.Manco, M.R.Faraone-Mennella, C.Ferreri, and C.Chatgilialoglu (2006).
Investigation of radical-based damage of RNase A in aqueous solution and lipid vesicles.
  Biopolymers, 81, 39-50.  
15728177 A.Merlino, L.Mazzarella, A.Carannante, A.Di Fiore, A.Di Donato, E.Notomista, and F.Sica (2005).
The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants.
  J Biol Chem, 280, 17953-17960.
PDB codes: 1yv4 1yv6 1yv7
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.  
15647261 D.Picone, A.Di Fiore, C.Ercole, M.Franzese, F.Sica, S.Tomaselli, and L.Mazzarella (2005).
The role of the hinge loop in domain swapping. The special case of bovine seminal ribonuclease.
  J Biol Chem, 280, 13771-13778.
PDB codes: 1y92 1y94
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.  
12945053 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2003).
Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
  Proteins, 53, 101-110.  
14675549 A.Vrielink, and N.Sampson (2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
  Curr Opin Struct Biol, 13, 709-715.  
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
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.