7VPF

Crystal structure of a novel putative sugar isomerase from the psychrophilic bacterium Paenibacillus sp. R4

Summary for 7VPF

• Entry DOI: 10.2210/pdb7vpf/pdb
• Descriptor: Xylose isomerase, CALCIUM ION, ZINC ION (3 entities in total)
• Functional Keywords: sugar isomerase, xylose isomeras, glucose isomerase, paenibacillus, psychrophilic bacteria, cold adaptation, isomerase
• Biological source: Paenibacillus sp. FSL H7-0331
• Total number of polymer chains: 2
• Total formula weight: 65441.16

Authors

Park, H.H.,Lee, J.H.,Kwon, S. (deposition date: 2021-10-16, release date: 2021-12-29, Last modification date: 2023-11-29)

Primary citation

Kwon, S.,Ha, H.J.,Kang, Y.J.,Sung, J.H.,Hwang, J.,Lee, M.J.,Lee, J.H.,Park, H.H.
Crystal structure of a novel putative sugar isomerase from the psychrophilic bacterium Paenibacillus sp. R4.
Biochem.Biophys.Res.Commun., 585:48-54, 2021

PubMed Abstract: Sugar isomerases (SIs) catalyze the reversible conversion of aldoses to ketoses. A novel putative SI gene has been identified from the genome sequence information on the psychrophilic bacterium Paenibacillus sp. R4. Here, we report the crystal structure of the putative SI from Paenibacillus sp. R4 (PbSI) at 2.98 Å resolution. It was found that the overall structure of PbSI adopts the triose-phosphate isomerase (TIM) barrel fold. PbSI was also identified to have two heterogeneous metal ions as its cofactors at the active site in the TIM barrel, one of which was confirmed as a Zn ion through X-ray anomalous scattering and inductively coupled plasma mass spectrometry analysis. Structural comparison with homologous SI proteins from mesophiles, hyperthermophiles, and a psychrophile revealed that key residues in the active site are well conserved and that dimeric PbSI is devoid of the extended C-terminal region, which tetrameric SIs commonly have. Our results provide novel structural information on the cold-adaptable SI, including information on the metal composition in the active site.

PubMed: 34784551
DOI: 10.1016/j.bbrc.2021.11.026

Experimental method

X-RAY DIFFRACTION (2.983 Å)