2Y24

STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY ERWINIA CHRYSANTHEMI GH5 GLUCURONOXYLANASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Basis for Substrate Recognition by Erwinia Chrysanthemi Gh30 Glucuronoxylanase.

Urbanikova, L.Vrsanska, M.Krogh, K.B.Hoff, T.Biely, P.

(2011) FEBS J 278: 2105

  • DOI: 10.1111/j.1742-4658.2011.08127.x
  • Primary Citation of Related Structures:  
    2Y24

  • PubMed Abstract: 
  • Xylanase A from the phytopathogenic bacterium Erwinia chrysanthemi is classified as a glycoside hydrolase family 30 enzyme (previously in family 5) and is specialized for degradation of glucuronoxylan. The recombinant enzyme was crystallized with the aldotetraouronic acid β-D-xylopyranosyl-(1→4)-[4-O-methyl-α-D-glucuronosyl-(1→2)]-β-D-xylopyranosyl-(1→4)-D-xylose as a ligand ...

    Xylanase A from the phytopathogenic bacterium Erwinia chrysanthemi is classified as a glycoside hydrolase family 30 enzyme (previously in family 5) and is specialized for degradation of glucuronoxylan. The recombinant enzyme was crystallized with the aldotetraouronic acid β-D-xylopyranosyl-(1→4)-[4-O-methyl-α-D-glucuronosyl-(1→2)]-β-D-xylopyranosyl-(1→4)-D-xylose as a ligand. The crystal structure of the enzyme-ligand complex was solved at 1.39 Å resolution. The ligand xylotriose moiety occupies subsites -1, -2 and -3, whereas the methyl glucuronic acid residue attached to the middle xylopyranosyl residue of xylotriose is bound to the enzyme through hydrogen bonds to five amino acids and by the ionic interaction of the methyl glucuronic acid carboxylate with the positively charged guanidinium group of Arg293. The interaction of the enzyme with the methyl glucuronic acid residue appears to be indispensable for proper distortion of the xylan chain and its effective hydrolysis. Such a distortion does not occur with linear β-1,4-xylooligosaccharides, which are hydrolyzed by the enzyme at a negligible rate.


    Organizational Affiliation

    Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XYLANASEA383Dickeya chrysanthemiMutation(s): 0 
EC: 3.2.1.8 (PDB Primary Data), 3.2.1.136 (PDB Primary Data)
UniProt
Find proteins for Q46961 (Dickeya chrysanthemi)
Explore Q46961 
Go to UniProtKB:  Q46961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46961
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranoseB 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14569KK
GlyCosmos:  G14569KK
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.578α = 90
b = 59.578β = 90
c = 168.296γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-12-21
    Changes: Database references, Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary