1OJR

L-rhamnulose-1-phosphate aldolase from Escherichia coli (mutant E192A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.111 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase.

Kroemer, M.Merkel, I.Schulz, G.E.

(2003) Biochemistry 42: 10560

  • DOI: 10.1021/bi0349266
  • Also Cited By: 2UYU, 2UYV, 2V29, 2V2A, 2V2B, 2V9E, 2V9F, 2V9G, 2V9I, 2V9L, 2V9M, 2V9N, 2V9O

  • PubMed Abstract: 
  • The structure of L-rhamnulose-1-phosphate aldolase has been established at 1.35 A resolution in a crystal form that was obtained by a surface mutation and has one subunit of the C(4)-symmetric tetramer in the asymmetric unit. It confirms an earlier 2 ...

    The structure of L-rhamnulose-1-phosphate aldolase has been established at 1.35 A resolution in a crystal form that was obtained by a surface mutation and has one subunit of the C(4)-symmetric tetramer in the asymmetric unit. It confirms an earlier 2.7 A resolution structure which was determined in a complicated crystal form with 20 subunits per asymmetric unit. The chain fold and the active center are similar to those of L-fuculose-1-phosphate aldolase and L-ribulose-5-phosphate 4-epimerase. The active center similarity is supported by a structural comparison of all three enzymes and by the binding mode of the inhibitor phosphoglycolohydroxamate at the site of the product dihydroxyacetone phosphate for the two aldolases. The sensitivity of the catalytic rate to several mutations and a comparison with the established mechanism of the related aldolase give rise to a putative catalytic mechanism. This mechanism involves the same binding mode of the second product L-lactaldehyde in both aldolases, except for a 180 degrees flip of the aldehyde group distinguishing between the two epimers rhamnulose and fuculose. The N-terminal domain exhibits a correlated anisotropic mobility that channels the isotropic Brownian motion into a directed movement of the catalytic base and the substrate phosphate on the N-domain toward the zinc ion and the lactaldehyde on the C-terminal domain. We suggest that this movement supports the catalysis mechanically.


    Related Citations: 
    • 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
    • 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
    • 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


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHAMNULOSE-1-PHOSPHATE ALDOLASE
A
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2HA
Query on 2HA

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Download CCD File 
A
DIHYDROXYACETONE
C3 H6 O3
RXKJFZQQPQGTFL-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

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A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.111 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.024α = 90.00
b = 108.024β = 90.00
c = 57.166γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance