2UYT

Structure of L-rhamnulose kinase in complex with ADP and beta-L- rhamnulose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate Spectrum of L-Rhamnulose Kinase Related to Models Derived from Two Ternary Complex Structures.

Grueninger, D.Schulz, G.E.

(2007) FEBS Lett. 581: 3127

  • DOI: 10.1016/j.febslet.2007.05.075

  • PubMed Abstract: 
  • The enzyme L-rhamnulose kinase from Escherichia coli participates in the degradation pathway of L-rhamnose, a common natural deoxy-hexose. The structure of the enzyme in a ternary complex with its substrates ADP and L-rhamnulose has been determined a ...

    The enzyme L-rhamnulose kinase from Escherichia coli participates in the degradation pathway of L-rhamnose, a common natural deoxy-hexose. The structure of the enzyme in a ternary complex with its substrates ADP and L-rhamnulose has been determined at 1.55A resolution and refined to R(cryst)/R(free) values of 0.179/0.209. The result was compared with the lower resolution structure of a corresponding complex containing L-fructose instead of L-rhamnulose. In light of the two established sugar positions and conformations, a number of rare sugars have been modeled into the active center of L-rhamnulose kinase and the model structures have been compared with the known enzymatic phosphorylation rates. Rare sugars are of rising interest for the synthesis of bioactive compounds.


    Related Citations: 
    • Structure and Reaction Mechanism of L-Rhamnulose Kinase from Escherichia Coli
      Grueninger, D.,Schulz, G.E.
      (2006) J.Mol.Biol. 359: 787


    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
RHAMNULOKINASE
A
489Escherichia coli (strain UTI89 / UPEC)Mutation(s): 3 
Gene Names: rhaB
EC: 2.7.1.5
Find proteins for Q1R415 (Escherichia coli (strain UTI89 / UPEC))
Go to UniProtKB:  Q1R415
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRH
Query on LRH

Download SDF File 
Download CCD File 
A
6-DEOXY-BETA-L-FRUCTOFURANOSE
C6 H12 O5
CJJCPDZKQKUXSS-AZGQCCRYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.043α = 90.00
b = 51.093β = 90.00
c = 158.850γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-10-24
    Type: Data collection, Source and taxonomy