1X8D

Crystal structure of E. coli YiiL protein containing L-rhamnose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Insights into the Monosaccharide Specificity of Escherichia coli Rhamnose Mutarotase

Ryu, K.S.Kim, J.I.Cho, S.J.Park, D.Park, C.Cheong, H.K.Lee, J.O.Choi, B.S.

(2005) J.Mol.Biol. 349: 153-162

  • DOI: 10.1016/j.jmb.2005.03.047

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli rhamnose mutarotase (YiiL) is completely different from the previously reported structures of the Lactococcus lactis galactose mutarotase and the Bacillus subtilis RbsD (pyranase). YiiL exists as a locally as ...

    The crystal structure of Escherichia coli rhamnose mutarotase (YiiL) is completely different from the previously reported structures of the Lactococcus lactis galactose mutarotase and the Bacillus subtilis RbsD (pyranase). YiiL exists as a locally asymmetric dimer, which is stabilized by an intermolecular beta-sheet, various hydrophobic interactions, and a cation-pi interaction with a salt-bridge. The protein folds of YiiL are similar to those of a Streptomyces coelicolor mono-oxygenase and a hypothetical Arabidopsis thaliana protein At3g17210. By assaying the enzymatic activity of six active-site mutants and by comparing the crystal structure-derived active site conformations of YiiL, RbsD, and a galactose mutarotase, we were able to define the amino acid residues required for catalysis and suggest a possible catalytic mechanism for YiiL. Although the active-site amino acid residues of YiiL (His, Tyr, and Trp) differ greatly from those of galactose mutarotase (His, Glu, and Asp), their geometries, which determine the structures of the preferred monosaccharide substrates, are conserved. In addition, the in vivo function of YiiL was assessed by constructing a mutant E.coli strain that carries a yiiL deletion. The presence of the yiiL gene is critical for efficient cell growth only when concentrations of l-rhamnose are limited.


    Organizational Affiliation

    Yusong-Gu, Yeoeun-Dong 52, Magnetic Resonance Team, Korea Basic Science Institute, Daejon 305-333, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein yiiL
A, B, C, D
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rhaM (yiiL)
EC: 5.1.3.32
Find proteins for P32156 (Escherichia coli (strain K12))
Go to UniProtKB:  P32156
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RNS
Query on RNS

Download SDF File 
Download CCD File 
A, B, C, D
L-RHAMNOSE
C6 H12 O5
PNNNRSAQSRJVSB-BXKVDMCESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RNSKd: 6160000 nM BINDINGMOAD
RNSKd: 6160000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.358α = 90.00
b = 51.311β = 107.82
c = 80.492γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-08-08
    Type: Data collection