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PDBsum entry 1eid

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Hydrolase PDB id
1eid
Jmol
Contents
Protein chain
124 a.a. *
Waters ×142
* Residue conservation analysis
PDB id:
1eid
Name: Hydrolase
Title: Crystal structure of f120g mutant of bovine pancreatic ribonuclease a
Structure: Ribonuclease a. Chain: a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.40Å     R-factor:   0.210     R-free:   0.265
Authors: E.Chatani,R.Hayashi,H.Moriyama,T.Ueki
Key ref: E.Chatani et al. (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. PubMed id: 11742124
Date:
25-Feb-00     Release date:   13-Feb-02    
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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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     6 terms  

 

 
Protein Sci 11:72-81 (2002)
PubMed id: 11742124  
 
 
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.
E.Chatani, R.Hayashi, H.Moriyama, T.Ueki.
 
  ABSTRACT  
 
The replacement of Phe120 with other hydrophobic residues causes a decrease in the activity and thermal stability in ribonuclease A (RNase A). To explain this, the crystal structures of wild-type RNase A and three mutants--F120A, F120G, and F120W--were analyzed up to a 1.4 A resolution. Although the overall backbone structures of all mutant samples were nearly the same as that of wild-type RNase A, except for the C-terminal region of F120G with a high B-factor, two local conformational changes were observed at His119 in the mutants. First, His119 of the wild-type and F120W RNase A adopted an A position, whereas those of F120A and F120G adopted a B position, but the static crystallographic position did not reflect either the efficiency of transphosphorylation or the hydrolysis reaction. Second, His119 imidazole rings of all mutant enzymes were deviated from that of wild-type RNase A, and those of F120W and F120G appeared to be "inside out" compared with that of wild-type RNase A. Only approximately 1 A change in the distance between N(epsilon2) of His12 and N(delta1) of His119 causes a drastic decrease in k(cat), indicating that the active site requires the strict positioning of the catalytic residues. A good correlation between the change in total accessible surface area of the pockets on the surface of the mutant enzymes and enthalpy change in their thermal denaturation also indicates that the effects caused by the replacements are not localized but extend to remote regions of the protein molecule.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22505256 P.V.Afonine, R.W.Grosse-Kunstleve, N.Echols, J.J.Headd, N.W.Moriarty, M.Mustyakimov, T.C.Terwilliger, A.Urzhumtsev, P.H.Zwart, and P.D.Adams (2012).
Towards automated crystallographic structure refinement with phenix.refine.
  Acta Crystallogr D Biol Crystallogr, 68, 352-367.  
20349493 C.Schulenburg, U.Weininger, P.Neumann, H.Meiselbach, M.T.Stubbs, H.Sticht, J.Balbach, R.Ulbrich-Hofmann, and U.Arnold (2010).
Impact of the C-terminal disulfide bond on the folding and stability of onconase.
  Chembiochem, 11, 978-986.
PDB codes: 2kb6 3fd7
  19851015 K.Homma, and H.Moriyama (2009).
Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1030-1034.
PDB codes: 3c2t 3c3i 3ca9
19588901 N.Doucet, E.D.Watt, and J.P.Loria (2009).
The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.
  Biochemistry, 48, 7160-7168.  
19373927 R.Vilà, A.Benito, M.Ribó, and M.Vilanova (2009).
Mapping the stability clusters in bovine pancreatic ribonuclease A.
  Biopolymers, 91, 1038-1047.  
18421168 L.Ito, T.Kobayashi, K.Shiraki, and H.Yamaguchi (2008).
Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A.
  J Synchrotron Radiat, 15, 316-318.  
17327674 C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, and M.S.Weiss (2007).
On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
  Acta Crystallogr D Biol Crystallogr, 63, 366-380.
PDB codes: 2g4h 2g4i 2g4j 2g4k 2g4l 2g4m 2g4n 2g4o 2g4p 2g4q 2g4r 2g4s 2g4t 2g4u 2g4v 2g4w 2g4x 2g4y 2g4z 2g51 2g52 2g55 2ill
17623866 K.S.Ghosh, T.K.Maiti, J.Debnath, and S.Dasgupta (2007).
Inhibition of Ribonuclease A by polyphenols present in green tea.
  Proteins, 69, 566-580.  
17384067 M.Noronha, J.C.Lima, E.Paci, H.Santos, and A.L.Maçanita (2007).
Tracking local conformational changes of ribonuclease A using picosecond time-resolved fluorescence of the six tyrosine residues.
  Biophys J, 92, 4401-4414.  
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.  
15858265 R.Caliandro, B.Carrozzini, G.L.Cascarano, L.De Caro, C.Giacovazzo, and D.Siliqi (2005).
Phasing at resolution higher than the experimental resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 556-565.  
16041073 R.Caliandro, B.Carrozzini, G.L.Cascarano, L.De Caro, C.Giacovazzo, and D.Siliqi (2005).
Ab initio phasing at resolution higher than experimental resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 1080-1087.  
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.