1NHC

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger.

van Pouderoyen, G., Snijder, H.J., Benen, J.A., Dijkstra, B.W.

(2003) FEBS Lett 554: 462-466

  • DOI: 10.1016/s0014-5793(03)01221-3
  • Primary Citation of Related Structures:  
    1NHC

  • PubMed Abstract: 

    • Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 A resolution crystal structure of endopolygalacturonase I reveals a narrowed substrate binding cleft. In addition, Arg96, a residue in this cleft previously shown to be critical for processivity, interacts with the substrate mimics glycerol and sulfate in several well-defined conformations in the six molecules in the asymmetric unit ...

    Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 A resolution crystal structure of endopolygalacturonase I reveals a narrowed substrate binding cleft. In addition, Arg96, a residue in this cleft previously shown to be critical for processivity, interacts with the substrate mimics glycerol and sulfate in several well-defined conformations in the six molecules in the asymmetric unit. From this we conclude that both Arg96 and the narrowed substrate binding cleft contribute to retaining the substrate while it moves through the active site after a cleavage event has occurred.

    Organizational Affiliation: 

    Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polygalacturonase IA, B, C, D, E, F336Aspergillus nigerMutation(s): 0 
Gene Names: pgaI, pg1, pga1
EC: 3.2.1.15
Find proteins for P26213 (Aspergillus niger)
Explore P26213 
Go to UniProtKB:  P26213
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH6 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
 HA [auth E], OA [auth F], V [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
MAN
Query on MAN
Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , FA [auth E] , GA [auth E] , J [auth A] , K [auth A] , NA [auth F] , O [auth B] , 
AA [auth D],  BA [auth D],  FA [auth E],  GA [auth E],  J [auth A],  K [auth A],  NA [auth F],  O [auth B],  P [auth B],  T [auth C],  U [auth C]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
CA [auth D] , DA [auth D] , IA [auth E] , JA [auth E] , KA [auth E] , L [auth A] , LA [auth E] , M [auth A] , 
CA [auth D],  DA [auth D],  IA [auth E],  JA [auth E],  KA [auth E],  L [auth A],  LA [auth E],  M [auth A],  PA [auth F],  Q [auth B],  QA [auth F],  R [auth B],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 EA [auth D], MA [auth E], N [auth A], RA [auth F], S [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.012α = 114.32
b = 84.13β = 98
c = 96.035γ = 89.75
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
EPMRphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary