1LF9

CRYSTAL STRUCTURE OF BACTERIAL GLUCOAMYLASE COMPLEXED WITH ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and evolution of prokaryotic glucoamylase

Aleshin, A.E.Feng, P.-H.Honzatko, R.B.Reilly, P.J.

(2003) J.Mol.Biol. 327: 61-73

  • Primary Citation of Related Structures:  1LF6

  • PubMed Abstract: 
  • The first crystal structures of a two-domain, prokaryotic glucoamylase were determined to high resolution from the clostridial species Thermoanaerobacterium thermosaccharolyticum with and without acarbose. The N-terminal domain has 18 antiparallel st ...

    The first crystal structures of a two-domain, prokaryotic glucoamylase were determined to high resolution from the clostridial species Thermoanaerobacterium thermosaccharolyticum with and without acarbose. The N-terminal domain has 18 antiparallel strands arranged in beta-sheets of a super-beta-sandwich. The C-terminal domain is an (alpha/alpha)(6) barrel, lacking the peripheral subdomain of eukaryotic glucoamylases. Interdomain contacts are common to all prokaryotic Family GH15 proteins. Domains similar to those of prokaryotic glucoamylases in maltose phosphorylases (Family GH65) and glycoaminoglycan lyases (Family PL8) suggest evolution from a common ancestor. Eukaryotic glucoamylases may have evolved from prokaryotic glucoamylases by the substitution of the N-terminal domain with the peripheral subdomain and by the addition of a starch-binding domain.


    Organizational Affiliation

    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOAMYLASE
A, B
684Thermoanaerobacterium thermosaccharolyticumGene Names: ga1
EC: 3.2.1.3
Find proteins for O85672 (Thermoanaerobacterium thermosaccharolyticum)
Go to UniProtKB:  O85672
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACR
Query on ACR

Download SDF File 
Download CCD File 
A, B
ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ACRKd: ~0.001 nM BINDINGMOAD
ACRKi: 0.001 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.491α = 90.00
b = 102.931β = 90.00
c = 164.686γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance