2V29

L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT K15W)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antenna Domain Mobility and Enzymatic Reaction of L-Rhamnulose-1-Phosphate Aldolase.

Grueninger, D.Schulz, G.E.

(2008) Biochemistry 47: 607

  • DOI: 10.1021/bi7012799
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzyme l-rhamnulose-1-phosphate aldolase from Escherichia coli participates in the degradation pathway of l-rhamnose, a ubiquitous deoxy-hexose. It is a homotetramer of the rare C4-symmetric type with N-terminal domains protruding like antennas f ...

    The enzyme l-rhamnulose-1-phosphate aldolase from Escherichia coli participates in the degradation pathway of l-rhamnose, a ubiquitous deoxy-hexose. It is a homotetramer of the rare C4-symmetric type with N-terminal domains protruding like antennas from the main body. A mobility analysis of the enzyme gave rise to the hypothesis that an anisotropic thermal antenna motion may support the catalysis (Kroemer et al., Biochemistry 42, 10560, 2003). We checked this hypothesis by generating four single mutants and one disulfide bridge that were designed to reduce the mobility of the antenna domain without disturbing the chain-fold or the active center. The catalytic rates of the mutants revealed activity reductions that correlated well with the expected antenna fixation. Among these mutants, K15W was crystallized, structurally elucidated, and used as a guide for modeling the others. The structure confirmed the design because the mutation introduced a tight nonpolar contact to a neighboring subunit that fixed the antenna but did not affect the main chain. The fixation was confirmed by a comparison of the anisotropic B-factors describing the mobility of the domains. It turned out that the distinctly anisotropic mobility of the wild-type antenna domain has become isotropic in K15W, in agreement with the design. We suggest that, like K15W, the other mutations also followed the design, validating the correlation between antenna mobility and activity. This correlation suggests that the domain mobility facilitates the reaction.


    Related Citations: 
    • Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase
      Kroemer, M.,Merkel, I.,Schulz, G.E.
      (2003) Biochemistry 42: 10560


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHAMNULOSE-1-PHOSPHATE ALDOLASE
A, B
274Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: rhaD (rhuA)
EC: 4.1.2.19
Find proteins for P32169 (Escherichia coli (strain K12))
Go to UniProtKB:  P32169
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 82.873α = 90.00
b = 82.873β = 90.00
c = 98.109γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance