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PDBsum entry 9rsa

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Hydrolase (phosphoric diester) PDB id
9rsa
Jmol
Contents
Protein chains
124 a.a. *
Ligands
ADU ×2
Waters ×181
* Residue conservation analysis
PDB id:
9rsa
Name: Hydrolase (phosphoric diester)
Title: Crystal structure of two covalent nucleoside derivatives of ribonuclease a
Structure: Ribonuclease a. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: s2. Organ: pancreas
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.196    
Authors: J.Nachman,A.Wlodawer
Key ref:
J.Nachman et al. (1990). Crystal structure of two covalent nucleoside derivatives of ribonuclease A. Biochemistry, 29, 928-937. PubMed id: 2340284 DOI: 10.1021/bi00456a012
Date:
28-Aug-89     Release date:   15-Apr-91    
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: 10.1021/bi00456a012 Biochemistry 29:928-937 (1990)
PubMed id: 2340284  
 
 
Crystal structure of two covalent nucleoside derivatives of ribonuclease A.
J.Nachman, M.Miller, G.L.Gilliland, R.Carty, M.Pincus, A.Wlodawer.
 
  ABSTRACT  
 
Crystal structures of two forms of ribonuclease A with deoxynucleosides covalently bound to respectively His 12 and His 119 have been solved. One form, T-H12-RNase, has a deoxythymidine bound to N epsilon 2 of His 12, while the other one, U-H119-RNase, has a deoxyuridine bound to N delta 1 of His 119. The two crystal forms are nearly isomorphous, with two molecules in the asymmetric unit. However, the modified ribonucleases differ both in their enzymatic activities and in the conformation of the catalytic site and of the deoxynucleoside-histidine moiety. T-H12-RNase is characterized by complete loss of enzymatic activity; in this form the deoxynucleoside completely blocks the catalytic site and forms intramolecular contacts with residues associated with both the B1 and B2 sites. U-H119-RNase retains 1% of the activity of the unmodified enzyme, and in this form His 119 adopts a different orientation, corresponding to the alternate conformation reported for this residue; the deoxynucleoside-histidine moiety points out of the active site and does not form any contacts with the rest of the protein, thus allowing partial access to the catalytic site. On the basis of these structures, we propose possible mechanisms for the reactions of bromoacetamido nucleosides with ribonuclease A.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481778 E.Karaca, and A.M.Bonvin (2011).
A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.
  Structure, 19, 555-565.  
  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
17729269 A.May, and M.Zacharias (2008).
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.
  Proteins, 70, 794-809.  
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.  
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
9011022 G.Ashkenazi, D.R.Ripoll, N.Lotan, and H.A.Scheraga (1997).
A molecular switch for biochemical logic gates: conformational studies.
  Biosens Bioelectron, 12, 85-95.  
9406542 J.Janin (1997).
Specific versus non-specific contacts in protein crystals.
  Nat Struct Biol, 4, 973-974.  
9135159 S.Y.Hsieh, T.P.Ko, M.Y.Tseng, W.Ku, K.F.Chak, and H.S.Yuan (1997).
A novel role of ImmE7 in the autoregulatory expression of the ColE7 operon and identification of possible RNase active sites in the crystal structure of dimeric ImmE7.
  EMBO J, 16, 1444-1454.
PDB code: 1unk
8789192 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
  J Comput Aided Mol Des, 9, 500-512.  
8710835 W.B.Church, A.Palmer, J.C.Wathey, and D.H.Kitson (1995).
Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: construction of models and comparison with experiment.
  Proteins, 23, 422-430.  
7704530 D.I.Liao, and O.Herzberg (1994).
Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.
  Structure, 2, 1203-1216.
PDB codes: 1sph 2hpr
  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
  8142897 V.S.deMel, M.S.Doscher, M.A.Glinn, P.D.Martin, M.L.Ram, and B.F.Edwards (1994).
Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases.
  Protein Sci, 3, 39-50.
PDB codes: 1ssa 1ssb
8394001 M.H.Zehfus (1993).
Improved calculations of compactness and a reevaluation of continuous compact units.
  Proteins, 16, 293-300.  
8464727 S.L.Moodie, and J.M.Thornton (1993).
A study into the effects of protein binding on nucleotide conformation.
  Nucleic Acids Res, 21, 1369-1380.  
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.