1GT7

L-rhamnulose-1-phosphate aldolase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of L-Rhamnulose-1-Phosphate Aldolase (Class II) Solved by Low-Resolution Sir Phasing and 20-Fold Ncs Averaging

Kroemer, M.Schulz, G.E.

(2002) Acta Crystallogr.,Sect.D 58: 824

  • Also Cited By: 1OJR

  • PubMed Abstract: 
  • The enzyme L-rhamnulose-1-phosphate aldolase catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde. It is a homotetramer with an M(r) of 30 000 per subunit and crystallized in space group P3(2) ...

    The enzyme L-rhamnulose-1-phosphate aldolase catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde. It is a homotetramer with an M(r) of 30 000 per subunit and crystallized in space group P3(2)21. The enzyme shows a low sequence identity of 18% with the structurally known L-fuculose-1-phosphate aldolase that splits a stereoisomer in a similar reaction. Structure analysis was initiated with a single heavy-atom derivative measured to 6 A resolution. The resulting poor electron density, a self-rotation function and the working hypothesis that both enzymes are C(4) symmetric with envelopes that resemble one another allowed the location of the 20 protomers of the asymmetric unit. The crystal-packing unit was a D(4)-symmetric propeller consisting of five D(4)-symmetric octamers around an internal crystallographic twofold axis. Presumably, the propellers associate laterally in layers, which in turn pile up along the 3(2) axis to form the crystal. The non-crystallographic symmetry was used to extend the phases to the 2.7 A resolution limit and to establish a refined atomic model of the enzyme. The structure showed that the two enzymes are indeed homologous and that they possess chemically similar active centres.


    Related Citations: 
    • Sequencing and Characterization of a Gene Cluster Encoding the Enzymes for L-Rhamnose Metabolism in Escherichia Coli
      Moralejo, P.,Egan, S.M.,Hidalgo, E.,Aguilar, J.
      (1993) J.Bacteriol. 175: 5585
    • Structures of L-Fuculose-1-Phosphate Aldolase Mutants Outlining Motions During Catalysis
      Joerger, A.C.,Mueller-Dieckmann, C.,Schulz, G.E.
      (2000) J.Mol.Biol. 303: 531


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, 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, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
274Escherichia coli (strain K12)Gene Names: rhaD (rhuA)
EC: 4.1.2.19
Find proteins for P32169 (Escherichia coli (strain K12))
Go to UniProtKB:  P32169
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 225.760α = 90.00
b = 225.760β = 90.00
c = 285.645γ = 120.00
Software Package:
Software NamePurpose
DMmodel building
GETAXphasing
SCALAdata scaling
SCALEITphasing
MLPHAREphasing
REFMACrefinement
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-03
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Derived calculations, Non-polymer description, Other, Version format compliance