1KCD

Endopolygalacturonase I from Stereum purpureum complexed with two galacturonate at 1.15 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.

Shimizu, T.Nakatsu, T.Miyairi, K.Okuno, T.Kato, H.

(2002) Biochemistry 41: 6651-6659

  • Primary Citation of Related Structures:  1K5C, 1KCC

  • PubMed Abstract: 
  • Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonat ...

    Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.


    Related Citations: 
    • Determination of glycosylation sites, disulfide bridges, and the C-terminus of Stereum purpureum mature endopolygalacturonase I by electrospray ionization mass spectrometry
      Shimizu, T.,Miyairi, K.,Okuno, T.
      (2000) Eur.J.Biochem. 267: 2380
    • Isolation, characterization, and sugar chain structure of endoPG Ia, Ib and Ic from Stereum purpureum
      Hasui, Y.,Fukui, Y.,Kikuchi, J.,Kato, N.,Miyairi, K.,Okuno, T.
      (1998) BIOSCI.BIOTECHNOL.BIOCHEM. 62: 852
    • Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum
      Shimizu, T.,Nakatsu, T.,Miyairi, K.,Okuno, T.,Kato, H.
      (2001) Acta Crystallogr.,Sect.D 57: 1171


    Organizational Affiliation

    Kinetic Crystallography Research Team, Membrane Dynamics Research Group, RIKEN, Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOPOLYGALACTURONASE
A
335Chondrostereum purpureumGene Names: cppg1
EC: 3.2.1.15
Find proteins for P79074 (Chondrostereum purpureum)
Go to UniProtKB:  P79074
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTR
Query on GTR

Download SDF File 
Download CCD File 
A
Beta-D-Galactopyranuronic acid
Galacturonic acid
C6 H10 O7
AEMOLEFTQBMNLQ-DTEWXJGMSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GTK
Query on GTK

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Download CCD File 
A
beta-D-galactofuranuronic acid
C6 H10 O7
OEVWLAOZEALENB-ORELYVPDSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.126 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.500α = 72.39
b = 52.070β = 69.50
c = 37.230γ = 70.54
Software Package:
Software NamePurpose
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-08-24
    Type: Non-polymer description
  • Version 1.4: 2015-10-14
    Type: Non-polymer description