6B3P

Crystal structure of CBMbc (family CBM26) from Eubacterium rectale Amy13K in Complex with Maltoheptaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel carbohydrate binding modules in the surface anchored alpha-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut.

Cockburn, D.W.Suh, C.Medina, K.P.Duvall, R.M.Wawrzak, Z.Henrissat, B.Koropatkin, N.M.

(2018) Mol. Microbiol. 107: 249-264

  • DOI: 10.1111/mmi.13881
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-produci ...

    Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-producing organism in the gut, consumes a limited range of substrates, including starch. Host consumption of resistant starch increases the abundance of E. rectale in the intestine, likely because it successfully captures the products of resistant starch degradation by other bacteria. Here, we demonstrate that the cell wall anchored starch-degrading α-amylase, Amy13K of E. rectale harbors five CBMs that all target starch with differing specificities. Intriguingly these CBMs efficiently bind to both regular and high amylose corn starch (a type of resistant starch), but have almost no affinity for potato starch (another type of resistant starch). Removal of these CBMs from Amy13K reduces the activity level of the enzyme toward corn starches by ∼40-fold, down to the level of activity toward potato starch, suggesting that the CBMs facilitate activity on corn starch and allow its utilization in vivo. The specificity of the Amy13K CBMs provides a molecular rationale for why E. rectale is able to only use certain starch types without the aid of other organisms.


    Organizational Affiliation

    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amy13K
A, B
209[Eubacterium] rectale M104/1Mutation(s): 0 
Find proteins for D4JJZ5 ([Eubacterium] rectale M104/1)
Go to UniProtKB:  D4JJZ5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.184 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 134.200α = 90.00
b = 134.200β = 90.00
c = 231.130γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of Michigan Gastrointestinal Peptides Research CenterUnited StatesDK034933
Department of Energy (United States)United StatesDE-AC02-06CH11357
Michigan Economic Development Corporation and the Michigan Technology Tri-CorridorUnited States085P1000817

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence
  • Version 1.2: 2018-01-17
    Type: Database references