1BAO

THE CONTRIBUTION OF BURIED HYDROGEN BONDS TO PROTEIN STABILITY: THE CRYSTAL STRUCTURES OF TWO BARNASE MUTANTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants.

Chen, Y.W.Fersht, A.R.Henrick, K.

(1993) J Mol Biol 234: 1158-1170

  • DOI: 10.1006/jmbi.1993.1667
  • Primary Citation of Related Structures:  
    1BAN, 1BAO, 1BNS

  • PubMed Abstract: 
  • The crystal structures of two barnase mutants, Tyr78-->Phe and Ser91-->Ala, have been determined to 2.2 A resolution. In both cases, a buried hydroxyl group that makes two hydrogen bonds within the protein was replaced by a hydrogen atom. It is found that neither mutation causes any structural changes, within the limits of error, compared with wild-type and so are confirmed to be non-disruptive ...

    The crystal structures of two barnase mutants, Tyr78-->Phe and Ser91-->Ala, have been determined to 2.2 A resolution. In both cases, a buried hydroxyl group that makes two hydrogen bonds within the protein was replaced by a hydrogen atom. It is found that neither mutation causes any structural changes, within the limits of error, compared with wild-type and so are confirmed to be non-disruptive. Solvent molecules are not observed in the cavities created by removal of the respective hydroxyl groups and no new interactions are introduced. The local water structure surrounding both sites of mutation is well conserved and resembles that of the wild-type. All four water molecules making contacts with the side-chain of residue 78 and two water molecules nearest to residue 91 in the wild-type are found within a sphere of 0.5 A radius, at the equivalent positions of the respective mutant. No new water molecules are found bound to any of the hydrogen bond donor or acceptor residues involved in these two mutation sites. Previous protein engineering experiments established that the solvent-inaccessible phenolic OH of Tyr78 that makes hydrogen bonds with two uncharged groups (main-chain NH and CO) contributes 1.4 kcal mol-1 to protein stability, while the solvent-inaccessible OH of Ser91 that makes hydrogen bonds with an uncharged main-chain NH and a charged group (O gamma 1) contributes 1.9 kcal mol-1. These stability measurements can now be attributed primarily to the loss of the hydrogen bonding interactions because both mutations neither disrupt the respective protein and local solvent structures, upset the overall hydrogen bonding pattern nor introduce new interactions. The mutations Tyr78-->Phe and Ser91-->Ala are thus good examples of "non-disruptive deletions" and the results of mutagenesis can be analysed at the simplest level.


    Related Citations: 
    • The Folding of an Enzyme. II. Substructure of Barnase and the Contribution of Different Interactions to Protein Stability
      Serrano, L., Kellis Junior, J.T., Cann, P., Matouschek, A., Fersht, A.R.
      (1992) J Mol Biol 224: 783
    • Molecular Structure of a New Family of Ribonucleases
      Mauguen, Y., Hartley, R.W., Dodson, E.J., Dodson, G.G., Bricogne, G., Chothia, C., Jack, A.
      (1982) Nature 297: 162

    Organizational Affiliation

    Centre for Protein Engineering, Medical Research Council Centre, Cambridge, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BARNASEA, B, C110Bacillus amyloliquefaciensMutation(s): 0 
EC: 3.1.27
UniProt
Find proteins for P00648 (Bacillus amyloliquefaciens)
Explore P00648 
Go to UniProtKB:  P00648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00648
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.152 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.809α = 90
b = 58.809β = 90
c = 81.902γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other