2GH9

Thermus thermophilus maltotriose binding protein bound with maltotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report



Literature

Structural adaptations that modulate monosaccharide, disaccharide, and trisaccharide specificities in periplasmic maltose-binding proteins.

Cuneo, M.J.Changela, A.Beese, L.S.Hellinga, H.W.

(2009) J Mol Biol 389: 157-166

  • DOI: 10.1016/j.jmb.2009.04.008
  • Primary Citation of Related Structures:  
    2GH9

  • PubMed Abstract: 
  • Periplasmic binding proteins comprise a superfamily that is present in archaea, prokaryotes, and eukaryotes. Periplasmic binding protein ligand-binding sites have diversified to bind a wide variety of ligands. Characterization of the structural mecha ...

    Periplasmic binding proteins comprise a superfamily that is present in archaea, prokaryotes, and eukaryotes. Periplasmic binding protein ligand-binding sites have diversified to bind a wide variety of ligands. Characterization of the structural mechanisms by which functional adaptation occurs is key to understanding the evolution of this important protein superfamily. Here we present the structure and ligand-binding properties of a maltotriose-binding protein identified from the Thermus thermophilus genome sequence. We found that this receptor has a high affinity for the trisaccharide maltotriose (K(d)<1 microM) but little affinity for disaccharides that are transported by a paralogous maltose transport operon present in T. thermophilus. Comparison of this structure to other proteins that adopt the maltose-binding protein fold but bind monosaccharides, disaccharides, or trisaccharides reveals the presence of four subsites that bind individual glucose ring units. Two loops and three helical segments encode adaptations that control the presence of each subsite by steric blocking or hydrogen bonding. We provide a model in which the energetics of long-range conformational equilibria controls subsite occupancy and ligand binding.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
maltose/maltodextrin-binding proteinA386Thermus thermophilus HB27Mutation(s): 0 
Gene Names: ttc1288TT_C1288
Find proteins for Q72I44 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72I44 
Go to UniProtKB:  Q72I44
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
3 N/A Oligosaccharides Interaction
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MLRKd:  1000   nM  Binding MOAD
MLRKd :  1000   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
Balpha-maltotrioseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.09α = 90
b = 68.994β = 90
c = 90.085γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary