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PDBsum entry 1rob

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Hydrolase(endoribonuclease) PDB id
1rob
Jmol
Contents
Protein chain
124 a.a. *
Ligands
C2P
Waters ×101
* Residue conservation analysis
PDB id:
1rob
Name: Hydrolase(endoribonuclease)
Title: Structure of the crystalline complex of cytidylic acid (2'- cmp) with ribonuclease at 1.6 angstroms resolution
Structure: Ribonuclease a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.60Å     R-factor:   0.170    
Authors: J.N.Lisgarten,R.A.Palmer
Key ref:
J.N.Lisgarten et al. (1993). Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 A resolution. Conservation of solvent sites in RNase-A high-resolution structures. Acta Crystallogr D Biol Crystallogr, 49, 541-547. PubMed id: 15299491 DOI: 10.1107/S090744499300719X
Date:
23-Aug-93     Release date:   31-Jan-94    
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/S090744499300719X Acta Crystallogr D Biol Crystallogr 49:541-547 (1993)
PubMed id: 15299491  
 
 
Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 A resolution. Conservation of solvent sites in RNase-A high-resolution structures.
J.N.Lisgarten, V.Gupta, D.Maes, L.Wyns, I.Zegers, R.A.Palmer, C.G.Dealwis, C.F.Aguilar, A.M.Hemmings.
 
  ABSTRACT  
 
The X-ray structure of the inhibitor complex of bovine ribonuclease A with cytidylic acid (2'-CMP) has been determined at 1.6 A resolution and refined by restrained least squares to R = 0.17 for 11 945 reflections. Binding of the inhibitor molecule to the protein is confirmed to be in the productive mode associated with enzyme activity. A study of conserved solvent sites amongst high-resolution structures in the same crystal form reveals a stabilizing water cluster between the N and C termini.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Electron density of the base, ribosą and phosphate and neighbouring protein groups.
Figure 5.
Fig. 5. Conserved solvent sites in five high-resolution RNase structures. The solvent cluster connecting the N-terminal a-helix with 110-121 loop is vis- ible on the right-hand side of the molecule. The active site resi- dues and the inhibitor are shown in red.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 541-547) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17957392 S.A.Gabel, and R.E.London (2008).
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry.
  J Biol Inorg Chem, 13, 207-217.  
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
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
16233267 N.Tanimizu, H.Ueno, and R.Hayashi (2002).
Replacement of His12 or His119 of bovine pancreatic ribonuclease A with acidic amino acid residues for the modification of activity and stability.
  J Biosci Bioeng, 94, 39-44.  
  10892814 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2000).
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.
  Protein Sci, 9, 1217-1225.
PDB codes: 1eos 1eow
10090281 V.Gupta, S.Muyldermans, L.Wyns, and D.M.Salunke (1999).
The crystal structure of recombinant rat pancreatic RNase A.
  Proteins, 35, 1.
PDB code: 1rra
  8844852 C.Toiron, C.González, M.Bruix, and M.Rico (1996).
Three-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',5'-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics.
  Protein Sci, 5, 1633-1647.  
  7756988 I.Zegers, D.Maes, M.H.Dao-Thi, F.Poortmans, R.Palmer, and L.Wyns (1994).
The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.
  Protein Sci, 3, 2322-2339.
PDB codes: 1rpf 1rpg 1rph
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.