1SNM

ACTIVE SITE MUTANT GLU-43 (RIGHT ARROW) ASP IN STAPHYLOCOCCAL NUCLEASE DISPLAYS NONLOCAL STRUCTURAL CHANGES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Active site mutant Glu-43 --> Asp in staphylococcal nuclease displays nonlocal structural changes.

Loll, P.J.Lattman, E.E.

(1990) Biochemistry 29: 6866-6873


  • PubMed Abstract: 
  • The crystal structure of the Glu-43----Asp mutant of staphylococcal nuclease complexed with Ca2+ and the inhibitor thymidine 3',5'-bisphosphate (pdTp) has been determined and refined by restrained least-squares methods to a conventional crystallograp ...

    The crystal structure of the Glu-43----Asp mutant of staphylococcal nuclease complexed with Ca2+ and the inhibitor thymidine 3',5'-bisphosphate (pdTp) has been determined and refined by restrained least-squares methods to a conventional crystallographic R value of 0.174 at a resolution of 1.74 A. Throughout most of the structure, the conformation of the backbone atoms of the mutant is similar to that of the wild-type protein; however, the seemingly conservative mutation Glu----Asp has significantly perturbed the structure of a loop adjacent to the active site, as well as giving rise to looser binding of the essential calcium ion and to a less extensive network of bound water molecules in the active site. Crystal contacts that extend into the active site have also been altered by this amino acid substitution. The changes caused by this mutation are considerably more drastic than would have been predicted and should serve as caveats to those who would draw conclusions about structure-function relationships on the basis of site-directed mutagenesis experiments in the absence of structural data.


    Related Citations: 
    • The Crystal Structure of the Ternary Complex of Staphylococcal Nuclease, Ca2+, and the Inhibitor pdTp, Refined at 1.65 Angstroms
      Loll, P.J.,Lattman, E.E.
      (1989) Proteins 5: 183


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMONUCLEASE PRECURSOR
A
149Staphylococcus aureusMutation(s): 1 
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: 1.74 Å
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 48.590α = 90.00
b = 48.590β = 90.00
c = 63.380γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-07-15
    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