1MMY

Crystal structure of galactose mutarotase from Lactococcus lactis complexed with D-quinovose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural and kinetic studies of sugar binding to galactose mutarotase from Lactococcus lactis.

Thoden, J.B.Kim, J.Raushel, F.M.Holden, H.M.

(2002) J Biol Chem 277: 45458-45465

  • DOI: 10.1074/jbc.M208395200
  • Primary Citation of Related Structures:  
    1MN0, 1MMX, 1MMU, 1MMZ, 1MMY

  • PubMed Abstract: 
  • Galactose mutarotase catalyzes the conversion of beta-D-galactose to alpha-D-galactose in the Leloir pathway for galactose metabolism. The high resolution x-ray structure of the dimeric enzyme from Lactococcus lactis was recently solved and shown to ...

    Galactose mutarotase catalyzes the conversion of beta-D-galactose to alpha-D-galactose in the Leloir pathway for galactose metabolism. The high resolution x-ray structure of the dimeric enzyme from Lactococcus lactis was recently solved and shown to be topologically similar to the 18-stranded, anti-parallel beta-motif observed for domain 5 of beta-galactosidase. In addition to determining the overall molecular fold of galactose mutarotase, this initial investigation also provided a detailed description of the electrostatic interactions between the enzyme and its physiologically relevant substrate, galactose. Specifically, the side chains of His-96 and His-170 were shown to be located within hydrogen bonding distance to the C-5 oxygen of the substrate, while the carboxylate of Glu-304 was positioned near the C-1 hydroxyl group of the sugar. On the basis of this initial study, a possible role for Glu-304 as the general acid/base group in catalysis was put forth. Here we describe the combined x-ray crystallographic and kinetic analyses of L. lactis galactose mutarotase complexed with D-glucose, D-fucose, D-quinovose, L-arabinose, or D-xylose. These investigations have revealed that there are several distinct binding modes for these sugars, which are dependent upon the spatial orientation of the C-4 hydroxyl group. In those sugars with the same C-4 hydroxyl group orientation as galactose, their C-1 hydroxyl groups are invariably located near Glu-304. For those sugars, which have the same C-4 hydroxyl group configuration as glucose, the C-1 hydroxyls are typically located near Asp-243. These different binding modes correlate with both the observed kinetic parameters and the presence or absence of a hydrogen bond between the guanidinium group of Arg-71 and the C-4 hydroxyl group of the sugar ligand.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, USA. JBThoden@facstaff.wisc.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldose 1-epimeraseA, B347Lactococcus lactisMutation(s): 1 
Gene Names: galM
EC: 5.1.3.3
Find proteins for Q9ZB17 (Lactococcus lactis)
Explore Q9ZB17 
Go to UniProtKB:  Q9ZB17
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6D
Query on G6D

Download CCD File 
A, B
alpha-D-quinovopyranose
C6 H12 O5
SHZGCJCMOBCMKK-DVKNGEFBSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.9α = 90
b = 76.3β = 90
c = 210.8γ = 90
Software Package:
Software NamePurpose
FRAMBOdata collection
SAINTdata reduction
TNTrefinement
SAINTdata scaling
TNTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary