1OID

5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Trapping a 96 Degree Domain Rotation in Two Distinct Conformations by Engineered Disulfide Bridges

Schultz-Heienbrok, R., Maier, T., Straeter, N.

(2004) Protein Sci. 13: 1811

  • DOI: 10.1110/ps.04629604
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5'-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed ( ...

    Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5'-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges. The mutant proteins have been expressed, purified, and crystallized, to structurally characterize the designed variants. The S228C, P513C is a double mutant crystallized in two different crystal forms with three independent conformers, which differ from each other by a rotation of up to 12 degrees of the C-terminal domain with respect to the N-terminal domain. This finding, as well as an analysis of the domain motion in the crystal, indicates that the enzyme still exhibits considerable residual domain flexibility. In the double mutant that was designed to trap the enzyme in the closed conformation, the structure analysis reveals an unexpected intermediate conformation along the 96 degrees rotation trajectory between the open and closed enzyme forms. A comparison of the five independent conformers analyzed in this study shows that the domain movement of the variant enzymes is characterized by a sliding movement of the residues of the domain interface along the interface, which is in contrast to a classical closure motion where the residues of the domain interface move perpendicular to the interface.

    Related Citations: 
    • E. Coli 5'-Nucleotidase Undergoes a Hinge-Bending Domain Rotation Resembling a Ball-and-Socket Motion
      Knoefel, T.,Straeter, N.
      (2001) J.Mol.Biol. 309: 255
    • X-Ray Structure of the Escherichia Coli Periplasmic 5'-Nucleotidase Containing a Dimetal Catalytic Site
      Knoefel, T.,Straeter, N.
      (1999) Nat.Struct.Mol.Biol. 6: 448

    Organizational Affiliation: 

    Biotechnologisch-Biomedizinisches Zentrum der Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN USHA
A, B
532Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: ushA
Find proteins for P07024 (Escherichia coli (strain K12))
Go to UniProtKB:  P07024
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI
Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.496α = 90.00
b = 93.708β = 97.71
c = 82.901γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
REFMACrefinement
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance