6INT

xylose isomerase from Paenibacillus sp. R4

Summary for 6INT

• Entry DOI: 10.2210/pdb6int/pdb
• Descriptor: Xylose isomerase, CALCIUM ION (3 entities in total)
• Functional Keywords: paenibacillus species, cold-active protein, isomerase
• Biological source: Paenibacillus sp. R4
• Total number of polymer chains: 8
• Total formula weight: 392464.15

Authors

Lee, J.H.,Lee, C.W.,Park, S. (deposition date: 2018-10-26, release date: 2019-01-16, Last modification date: 2023-11-22)

Primary citation

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.
Crystal Structure and Functional Characterization of a Xylose Isomerase (PbXI) from the Psychrophilic Soil Microorganism, Paenibacillus sp.
J. Microbiol. Biotechnol., 29:244-255, 2019

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 (XI) from the psychrophilic soil microorganism, sp. R4. Surprisingly, activity assay results showed that XI is not a cold-active enzyme, but displays optimal activity at 60°C. We solved the crystal structure of XI at 1.94-Å resolution to investigate the origin of its thermostability. The XI structure shows a (β/α)-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 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.

PubMed: 30602271
DOI: 10.4014/jmb.1810.10057

Experimental method

X-RAY DIFFRACTION (1.942 Å)