6INT

xylose isomerase from Paenibacillus sp. R4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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This is version 1.1 of the entry. See complete history. 


Literature

Crystal Structure and Functional Characterization of a Xylose Isomerase (PbXI) from the Psychrophilic Soil Microorganism, Paenibacillus sp.

Park, S.H., Kwon, S., Lee, C.W., Kim, C.M., Jeong, C.S., Kim, K.J., Hong, J.W., Kim, H.J., Park, H.H., Lee, J.H.

(2019) J Microbiol Biotechnol 29: 244-255

  • DOI: https://doi.org/10.4014/jmb.1810.10057
  • Primary Citation of Related Structures:  
    6INT

  • PubMed Abstract: 

    • Xylose isomerase (XI; E.C. 5.3.1.5) catalyzes the isomerization of xylose to xylulose, which can be used to produce bioethanol through fermentation. Therefore, XI has recently gained attention as a key catalyst in the bioenergy industry. Here, we identified, purified, and characterized a XI ( Pb XI) from the psychrophilic soil microorganism, Paenibacillus sp ...

    Xylose isomerase (XI; E.C. 5.3.1.5) catalyzes the isomerization of xylose to xylulose, which can be used to produce bioethanol through fermentation. Therefore, XI has recently gained attention as a key catalyst in the bioenergy industry. Here, we identified, purified, and characterized a XI ( Pb XI) from the psychrophilic soil microorganism, Paenibacillus sp. R4. Surprisingly, activity assay results showed that Pb XI is not a cold-active enzyme, but displays optimal activity at 60°C. We solved the crystal structure of Pb XI at 1.94-Å resolution to investigate the origin of its thermostability. The Pb XI structure shows a (β/α) 8 -barrel fold with tight tetrameric interactions and it has three divalent metal ions (CaI, CaII, and CaIII). Two metal ions (CaI and CaII) located in the active site are known to be involved in the enzymatic reaction. The third metal ion (CaIII), located near the β4-α6 loop region, was newly identified and is thought to be important for the stability of Pb XI. Compared with previously determined thermostable and mesophilic XI structures, the β1-α2 loop structures near the substrate binding pocket of PbXI were remarkably different. Site-directed mutagenesis studies suggested that the flexible β1-α2 loop region is essential for PbXI activity. Our findings provide valuable insights that can be applied in protein engineering to generate lowtemperature purpose-specific XI enzymes.

    Organizational Affiliation: 

    Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xylose isomerase
A, B, C, D, E
A, B, C, D, E, F, G, H
438Paenibacillus sp. R4Mutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for A0A4V8H014 (Paenibacillus sp. R4)
Explore A0A4V8H014 
Go to UniProtKB:  A0A4V8H014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V8H014
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
CA [auth G]
DA [auth H]
EA [auth H]
AA [auth G],
BA [auth G],
CA [auth G],
DA [auth H],
EA [auth H],
FA [auth H],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D],
U [auth E],
V [auth E],
W [auth E],
X [auth F],
Y [auth F],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.282α = 90
b = 124.039β = 90
c = 315.001γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references