6L8P

Crystal structure of RidA from Antarctic bacterium Psychrobacter sp. PAMC 21119

Summary for 6L8P

• Entry DOI: 10.2210/pdb6l8p/pdb
• Descriptor: RidA family protein, MALONATE ION (3 entities in total)
• Functional Keywords: rida, deamination, psychrophile, antarctic bacterium, cold-adaptability, hydrolase
• Biological source: Psychrobacter sp. MES7-P7E
• Total number of polymer chains: 3
• Total formula weight: 47302.84

Authors

Kwon, S.,Lee, C.W.,Koh, H.Y.,Lee, J.H.,Park, H.H. (deposition date: 2019-11-06, release date: 2019-12-18, Last modification date: 2023-11-22)

Primary citation

Kwon, S.,Lee, C.W.,Koh, H.Y.,Park, H.,Lee, J.H.,Park, H.H.
Crystal structure of the reactive intermediate/imine deaminase A homolog from the Antarctic bacterium Psychrobacter sp. PAMC 21119.
Biochem.Biophys.Res.Commun., 522:585-591, 2020

PubMed Abstract: The RidA subfamily proteins catalyze the deamination reaction of enamine/imine intermediates, which are metabolites of amino acids such as threonine and serine. Numerous structural and functional studies have been conducted on RidA isolated from mesophiles and thermophiles. However, little is known about the structure of the RidA proteins isolated from psychrophiles. In the present study, we elucidated the crystal structure of RidA from the Antarctic bacterium Psychrobacter sp. PAMC 21119 (Pp-RidA) at 1.6 Å resolution to identify the structural properties contributing to cold-adaptability. Although the overall structure of Pp-RidA is similar to those of its homologues, it exhibits specific structural arrangements of a loop positioned near the active site, which is assumed to play a role in covering the active site of catalysis. In addition, the surface electrostatic potential of Pp-RidA suggested that it exhibits stronger electrostatic distribution relative to its homologues. Our results provide novel insights into the key determinants of cold-adaptability.

PubMed: 31785813
DOI: 10.1016/j.bbrc.2019.11.139

Experimental method

X-RAY DIFFRACTION (1.601 Å)