5K2M

Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA

Summary for 5K2M

• Entry DOI: 10.2210/pdb5k2m/pdb
• Related: 3VPB 3VPC 3VPD
• Descriptor: RimK-related lysine biosynthesis protein, Probable lysine biosynthesis protein, ADENOSINE-5'-DIPHOSPHATE, ... (9 entities in total)
• Functional Keywords: atp-dependent amine/thiol ligase family amino-group carrier protein lysine biosynthesis arginine biosynthesis, biosynthetic protein
• Biological source: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1); More
• Total number of polymer chains: 14
• Total formula weight: 284703.88

Authors

Yoshida, A.,Tomita, T.,Nishiyama, M. (deposition date: 2016-05-19, release date: 2016-09-07, Last modification date: 2023-11-29)

Primary citation

Yoshida, A.,Tomita, T.,Atomi, H.,Kuzuyama, T.,Nishiyama, M.
Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
J. Biol. Chem., 291:21630-21643, 2016

PubMed Abstract: We recently discovered a biosynthetic system using a novel amino group carrier protein called LysW for lysine biosynthesis via α-aminoadipate (AAA), and revealed that this system is also utilized in the biosynthesis of arginine by Sulfolobus In the present study, we focused on the biosynthesis of lysine and ornithine in the hyperthermophilic archaeon Thermococcus kodakarensis, and showed that their biosynthesis is accomplished by a single set of metabolic enzymes. We also determined the crystal structure of the LysX family protein from T. kodakarensis, which catalyzes the conjugation of LysW with either AAA or glutamate, in a complex with LysW-γ-AAA. This crystal structure is the first example to show how LysX recognizes AAA as a substrate and provides a structural basis for the bifunctionality of the LysX family protein from T. kodakarensis Based on comparisons with other LysX family proteins, we propose a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities.

PubMed: 27566549
DOI: 10.1074/jbc.M116.743021

Experimental method

X-RAY DIFFRACTION (2.18 Å)