1STA

ACCOMMODATION OF INSERTION MUTATIONS ON THE SURFACE AND IN THE INTERIOR OF STAPHYLOCOCCAL NUCLEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease.

Keefe, L.J.Quirk, S.Gittis, A.Sondek, J.Lattman, E.E.

(1994) Protein Sci. 3: 391-401

  • DOI: 10.1002/pro.5560030303
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alignment of homologous amino acid sequences reveals that insertion mutations are fairly common in evolution. Hitherto, the structural consequences of insertion mutations on the surface and in the interior of proteins of known structures have receive ...

    Alignment of homologous amino acid sequences reveals that insertion mutations are fairly common in evolution. Hitherto, the structural consequences of insertion mutations on the surface and in the interior of proteins of known structures have received little attention. We report here the high-resolution X-ray crystal structures of 2 site-directed insertion mutants of staphylococcal nuclease. The structure of the first insertion mutant, in which 2 glycine residues were inserted on the protein surface in the amino-terminal beta-strand, has been solved to 1.70 A resolution and refined to a crystallographic R value of 0.182. The inserted residues are accommodated in a special 3-residue beta-bulge. A bridging water molecule in the newly created cavity satisfies the hydrogen bonding requirements of the beta-sheet by forming a bifurcated hydrogen bond to 1 beta-strand, and a single hydrogen bond to the other beta-strand. The second insertion mutant contains a single leucine residue inserted at the end of the third beta-strand. The structure was solved to 2.0 A resolution and refined to a final R value of 0.196. The insertion is accommodated in a register shift that changes the conformation of the flexible loop portion of the molecule, relaxing and widening the omega turn. This structural alteration results in changes in position and coordination of a bound calcium ion important for catalysis. These structures illustrate important differences in how amino acid insertions are accommodated: as localized bulges, and as extensive register shifts.


    Related Citations: 
    • The Alpha Aneurism: A Structural Motif Revealed in an Insertion Mutant of Staphylococcal Nuclease
      Keefe, L.J.,Sondek, J.,Shortle, D.,Lattman, E.E.
      (1993) Proc.Natl.Acad.Sci.USA 90: 3275


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STAPHYLOCOCCAL NUCLEASE
A
151Staphylococcus aureusMutation(s): 0 
Gene Names: nuc
EC: 3.1.31.1
Find proteins for P00644 (Staphylococcus aureus)
Go to UniProtKB:  P00644
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
THP
Query on THP

Download SDF File 
Download CCD File 
A
THYMIDINE-3',5'-DIPHOSPHATE
C10 H16 N2 O11 P2
CSNCBOPUCJOHLS-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.182 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 47.896α = 90.00
b = 47.896β = 90.00
c = 62.998γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other