3KL0

Crystal structure of the glucuronoxylan xylanohydrolase XynC from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase.

St John, F.J.Hurlbert, J.C.Rice, J.D.Preston, J.F.Pozharski, E.

(2011) J Mol Biol 407: 92-109

  • DOI: https://doi.org/10.1016/j.jmb.2011.01.010
  • Primary Citation of Related Structures:  
    3KL0, 3KL3, 3KL5

  • PubMed Abstract: 

    Xylanases of glycosyl hydrolase family 30 (GH30) have been shown to cleave β-1,4 linkages of 4-O-methylglucuronoxylan (MeGX(n)) as directed by the position along the xylan chain of an α-1,2-linked 4-O-methylglucuronate (MeGA) moiety. Complete hydrolysis of MeGX(n) by these enzymes results in singly substituted aldouronates having a 4-O-methylglucuronate moiety linked to a xylose penultimate from the reducing terminal xylose and some number of xylose residues toward the nonreducing terminus. This novel mode of action distinguishes GH30 xylanases from the more common xylanase families that cleave MeGX(n) in accessible regions. To help understand this unique biochemical function, we have determined the structure of XynC in its native and ligand-bound forms. XynC structure models derived from diffraction data of XynC crystal soaks with the simple sugar glucuronate (GA) and the tetrameric sugar 4-O-methyl-aldotetrauronate resulted in models containing GA and 4-O-methyl-aldotriuronate, respectively. Each is observed in two locations within XynC surface openings. Ligand coordination occurs within the XynC catalytic substrate binding cleft and on the structurally fused side β-domain, demonstrating a substrate targeting role for this putative carbohydrate binding module. Structural data reveal that GA acts as a primary functional appendage for recognition and hydrolysis of the MeGX(n) polymer by the protein. This work compares the structure of XynC with a previously reported homologous enzyme, XynA, from Erwinia chrysanthemi and analyzes the ligand binding sites. Our results identify the molecular interactions that define the unique function of XynC and homologous GH30 enzymes.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA. fjstjohn@gmail.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucuronoxylanase xynC
A, B, C, D
401Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU18150xynCynfF
EC: 3.2.1.136
UniProt
Find proteins for Q45070 (Bacillus subtilis (strain 168))
Explore Q45070 
Go to UniProtKB:  Q45070
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45070
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HIS
Query on HIS

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
TAR
Query on TAR

Download Ideal Coordinates CCD File 
G [auth A]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
MLA
Query on MLA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
M [auth C],
O [auth D]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth C],
P [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.49α = 90
b = 195.796β = 90
c = 66.246γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary