4HU8

Crystal Structure of a Bacterial Ig-like Domain Containing GH10 Xylanase from Termite Gut


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biochemical characterization and crystal structure of a GH10 xylanase from termite gut bacteria reveal a novel structural feature and significance of its bacterial Ig-like domain.

Han, Q.Liu, N.Robinson, H.Cao, L.Qian, C.Wang, Q.Xie, L.Ding, H.Wang, Q.Huang, Y.Li, J.Zhou, Z.

(2013) Biotechnol Bioeng 110: 3093-3103

  • DOI: https://doi.org/10.1002/bit.24982
  • Primary Citation of Related Structures:  
    4HU8

  • PubMed Abstract: 

    Bacterial Ig-like (Big) domains are commonly distributed in glycoside hydrolases (GH), but their structure and function remains undefined. Xylanase is a GH, and catalyzes the hydrolysis of the internal β-xylosidic linkages of xylan. In this study, we report the molecular cloning, biochemical and biophysical characterization, and crystal structure of a termite gut bacterial xylanase, Xyl-ORF19, which was derived from gut bacteria of a wood-feeding termite (Globitermes brachycerastes). The protein architecture of Xyl-ORF19 reveals that it has two domains, a C-terminal GH10 catalytic domain and an N-terminal Big_2 non-catalytic domain. The catalytic domain folds in an (α/β)8 barrel as most GH10 xylanases do, but it has two extra β-strands. The non-catalytic domain is structurally similar to an immunoglobulin-like domain of intimins. The recombinant enzyme without the non-catalytic domain has fairly low catalytic activity, and is different from the full-length enzyme in kinetic parameters, pH and temperature profiles, which suggests the non-catalytic domain could affect the enzyme biochemical and biophysical properties as well as the role for enzyme localization. This study provides a molecular basis for future efforts in xylanase bioengineering.


  • Organizational Affiliation

    Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, 24061.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GH10 Xylanase
A, B, C, D, E
A, B, C, D, E, F, G, H
456Globitermes brachycerastesMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for K7PDC1 (uncultured bacterium 35A20)
Explore K7PDC1 
Go to UniProtKB:  K7PDC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7PDC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth H]
CA [auth H]
I [auth A]
K [auth B]
L [auth B]
BA [auth H],
CA [auth H],
I [auth A],
K [auth B],
L [auth B],
N [auth C],
R [auth D],
S [auth D],
U [auth E],
W [auth F],
X [auth F],
Y [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
EA [auth H]
J [auth A]
M [auth B]
AA [auth G],
DA [auth H],
EA [auth H],
J [auth A],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
T [auth D],
V [auth E],
Z [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.685α = 92.96
b = 86.963β = 90.86
c = 246.433γ = 108.56
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description