1DMB

REFINED 1.8 ANGSTROMS STRUCTURE REVEALS THE MECHANISM OF BINDING OF A CYCLIC SUGAR, BETA-CYCLODEXTRIN, TO THE MALTODEXTRIN BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined 1.8-A structure reveals the mode of binding of beta-cyclodextrin to the maltodextrin binding protein.

Sharff, A.J.Rodseth, L.E.Quiocho, F.A.

(1993) Biochemistry 32: 10553-10559


  • PubMed Abstract: 
  • The maltodextrin binding protein from Escherichia coli serves as the initial receptor for both the active transport of and chemotaxis toward a range of linear maltose sugars. The X-ray structures of both the maltose-bound and sugar-free forms of the ...

    The maltodextrin binding protein from Escherichia coli serves as the initial receptor for both the active transport of and chemotaxis toward a range of linear maltose sugars. The X-ray structures of both the maltose-bound and sugar-free forms of the protein have been previously described [Spurlino, J. C., Lu, G.-Y., & Quiocho, F. A. (1991) J. Biol. Chem. 266, 5202-5219; Sharff, A. J., Rodseth, L. E., Spurlino, J. C., & Quocho, F. A. (1992) Biochemistry 31, 10657-10663]. The X-ray crystal structure of the maltodextrin binding protein complexed with cyclomaltoheptaose (beta-cyclodextrin) has been determined from a single crystal. The structure has been refined to a final R-value of 21% at 1.8-A resolution. Although not a physiological ligand for the maltodextrin binding protein, beta-cyclodextrin has been shown to bind with a Kd of the same order as those of the linear maltodextrin substrates. The observed structure shows that the complexed protein remains in the fully open conformation and is almost identical to the structure of the unliganded protein. The sugar sits in the open cleft with three glucosyl units bound to the C-domain at the base of the cleft, in a similar position to maltotriose, the most tightly bound ligand. The top of the ring is loosely bound to the upper edge of the cleft on the N-domain. The sugar makes a total of 94 productive interactions (of less than 4.0-A length) with the protein and with bound water molecules.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • The 2.3 Angstroms Resolution Structure of the Maltose-or Maltodextrin-Binding Protein, a Primary Receptor of Bacterial Active Transport and Chemotaxis
      Spurlino, J.C.,Lu, G.-Y.,Quiocho, F.A.
      (1991) J.Biol.Chem. 266: 5202
    • Crystallographic Evidence of a Large Ligand-Induced Hinge-Twist Motion between the Two Domains of the Maltodextrin Binding Protein Involved in Active Transport and Chemotaxis
      Sharff, A.J.,Rodseth, L.E.,Spurlino, J.C.,Quiocho, F.A.
      (1992) Biochemistry 31: 10657


    Organizational Affiliation

    Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-MALTODEXTRIN BINDING PROTEIN
A
370Escherichia coli (strain K12)Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCD
Query on BCD

Download SDF File 
Download CCD File 
A
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCDKd: 1800 nM BINDINGMOAD
BCDKd: 1800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.210 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.860α = 101.50
b = 44.320β = 99.30
c = 58.310γ = 102.20
Software Package:
Software NamePurpose
X-PLORrefinement
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance