1UC9

Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8

Summary for 1UC9

• Entry DOI: 10.2210/pdb1uc9/pdb
• Related: 1UC8
• Descriptor: lysine biosynthesis enzyme, ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: lysine biosynthesis, alpha-aminoadipate pathway, riken structural genomics/proteomics initiative, rsgi, structural genomics, biosynthetic protein
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 61704.88

Authors

Sakai, H.,Vassylyeva, M.N.,Matsuura, T.,Sekine, S.,Nishiyama, M.,Terada, T.,Shirouzu, M.,Kuramitsu, S.,Vassylyev, D.G.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-04-09, release date: 2003-09-23, Last modification date: 2023-12-27)

Primary citation

Sakai, H.,Vassylyeva, M.N.,Matsuura, T.,Sekine, S.,Gotoh, K.,Nishiyama, M.,Terada, T.,Shirouzu, M.,Kuramitsu, S.,Vassylyev, D.G.,Yokoyama, S.
Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8
J.Mol.Biol., 332:729-740, 2003

PubMed Abstract: The thermophilic bacterium Thermus thermophilus synthesizes lysine through the alpha-aminoadipate pathway, which uses alpha-aminoadipate as a biosynthetic intermediate of lysine. LysX is the essential enzyme in this pathway, and is believed to catalyze the acylation of alpha-aminoadipate. We have determined the crystal structures of LysX and its complex with ADP at 2.0A and 2.38A resolutions, respectively. LysX is composed of three alpha+beta domains, each composed of a four to five-stranded beta-sheet core flanked by alpha-helices. The C-terminal and central domains form an ATP-grasp fold, which is responsible for ATP binding. LysX has two flexible loop regions, which are expected to play an important role in substrate binding and protection. In spite of the low level of sequence identity, the overall fold of LysX is surprisingly similar to that of other ATP-grasp fold proteins, such as D-Ala:D-Ala ligase, PurT-encoded glycinamide ribonucleotide transformylase, glutathione synthetase, and synapsin I. In particular, they share a similar spatial arrangement of the amino acid residues around the ATP-binding site. This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity.

PubMed: 12963379
DOI: 10.1016/S0022-2836(03)00946-X

Experimental method

X-RAY DIFFRACTION (2.38 Å)