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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.240 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8

Sakai, H.Vassylyeva, M.N.Matsuura, T.Sekine, S.Gotoh, K.Nishiyama, M.Terada, T.Shirouzu, M.Kuramitsu, S.Vassylyev, D.G.Yokoyama, S.

(2003) J Mol Biol 332: 729-740

  • DOI: https://doi.org/10.1016/s0022-2836(03)00946-x
  • Primary Citation of Related Structures:  
    1UC8, 1UC9

  • 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.

  • Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lysine biosynthesis enzyme
A, B
280Thermus thermophilusMutation(s): 0 
Find proteins for Q5SH23 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SH23 
Go to UniProtKB:  Q5SH23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SH23
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.652α = 90
b = 51.366β = 122.81
c = 103.594γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references