2OWX

THERMUS THERMOPHILUS AMYLOMALTASE AT pH 5.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three-way stabilization of the covalent intermediate in amylomaltase, an alpha-amylase-like transglycosylase.

Barends, T.R.Bultema, J.B.Kaper, T.van der Maarel, M.J.Dijkhuizen, L.Dijkstra, B.W.

(2007) J.Biol.Chem. 282: 17242-17249

  • DOI: 10.1074/jbc.M701444200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amylomaltases are glycosyl hydrolases belonging to glycoside hydrolase family 77 that are capable of the synthesis of large cyclic glucans and the disproportionation of oligosaccharides. Using protein crystallography, we have generated a flip book mo ...

    Amylomaltases are glycosyl hydrolases belonging to glycoside hydrolase family 77 that are capable of the synthesis of large cyclic glucans and the disproportionation of oligosaccharides. Using protein crystallography, we have generated a flip book movie of the amylomaltase catalytic cycle in atomic detail. The structures include a covalent glycosyl enzyme intermediate and a covalent intermediate in complex with an analogue of a co-substrate and show how the structures of both enzyme and substrate respond to the changes required by the catalytic cycle as it proceeds. Notably, the catalytic nucleophile changes conformation dramatically during the reaction. Also, Gln-256 on the 250s loop is involved in orienting the substrate in the +1 site. The absence of a suitable base in the covalent intermediate structure explains the low hydrolysis activity.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-alpha-glucanotransferase
A
503Thermus thermophilusMutation(s): 0 
Gene Names: malQ
EC: 2.4.1.25
Find proteins for O87172 (Thermus thermophilus)
Go to UniProtKB:  O87172
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SUI
Query on SUI
A
L-PEPTIDE LINKINGC6 H8 N2 O4ASP, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.801α = 90.00
b = 93.801β = 90.00
c = 154.769γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description