5E6Z

Crystal structure of Ecoli Branching Enzyme with beta cyclodextrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.878 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of Escherichia coli branching enzyme in complex with cyclodextrins.

Feng, L.Fawaz, R.Hovde, S.Sheng, F.Nosrati, M.Geiger, J.H.

(2016) Acta Crystallogr D Struct Biol 72: 641-647

  • DOI: 10.1107/S2059798316003272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Branching enzyme (BE) is responsible for the third step in glycogen/starch biosynthesis. It catalyzes the cleavage of α-1,4 glucan linkages and subsequent reattachment to form α-1,6 branch points. These branches are crucial to the final structure of ...

    Branching enzyme (BE) is responsible for the third step in glycogen/starch biosynthesis. It catalyzes the cleavage of α-1,4 glucan linkages and subsequent reattachment to form α-1,6 branch points. These branches are crucial to the final structure of glycogen and starch. The crystal structures of Escherichia coli BE (EcBE) in complex with α-, β- and γ-cyclodextrin were determined in order to better understand substrate binding. Four cyclodextrin-binding sites were identified in EcBE; they were all located on the surface of the enzyme, with none in the vicinity of the active site. While three of the sites were also identified as linear polysaccharide-binding sites, one of the sites is specific for cyclodextrins. In previous work three additional binding sites were identified as exclusively binding linear malto-oligosaccharides. Comparison of the binding sites shed light on this apparent specificity. Binding site IV is located in the carbohydrate-binding module 48 (CBM48) domain of EcBE and superimposes with the cyclodextrin-binding site found in the CBM48 domain of 5'-AMP-activated protein kinase (AMPK). Comparison of these sites shows the similarities and differences in the two binding modes. While some of the binding sites were found to be conserved between branching enzymes of different organisms, some are quite divergent, indicating both similarities and differences between oligosaccharide binding in branching enzymes from various sources.


    Organizational Affiliation

    Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,4-alpha-glucan branching enzyme GlgB
A, B, C, D
612Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: glgB
EC: 2.4.1.18
Find proteins for A7ZSW5 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZSW5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCD
Query on BCD

Download SDF File 
Download CCD File 
A, B, C, D
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.878 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.952α = 90.00
b = 102.995β = 91.57
c = 186.239γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references