PDBsum entry 3vpd

Ligase

PDB id: 3vpd

Contents

Protein chains

281 a.a.

Ligands

ANP ×2

BUA ×2

CIT

Waters ×418

PDB id:

3vpd

Name:

Ligase

Title:

Lysx from thermus thermophilus complexed with amp-pnp

Structure:

Ribosomal protein s6 modification protein. Chain: a, b. Synonym: ttlysx, rimk. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Gene: lysx, rimk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.95Å R-factor: 0.198 R-free: 0.238

Authors:

T.Tomita,T.Ouchi,T.Kuzuyama,M.Nishiyama

Key ref:

T.Ouchi et al. (2013). Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat Chem Biol, 9, 277-283. PubMed id: 23434852 DOI: 10.1038/nchembio.1200

Date:

29-Feb-12 Release date: 27-Feb-13

Protein chains

Q5SH23  (LYSX_THET8) -  Alpha-aminoadipate--LysW ligase LysX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 280 a.a.

Struc: 281 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.6.3.2.43 - [amino-group carrier protein]--L-2-aminoadipate ligase.
• Reaction: [amino-group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate + ATP = [amino-group carrier protein]-C-terminal-N-(1,4-dicarboxybutan-1- yl)-L-glutamine + ADP + phosphate + H⁺

[amino-group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate + ATP (Bound ligand (Het Group name = CIT) matches with 41.18% similarity) = [amino-group carrier protein]-C-terminal-N-(1,4-dicarboxybutan-1- yl)-L-glutamine + ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nchembio.1200

Nat Chem Biol 9:277-283 (2013)

PubMed id: 23434852

Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.

T.Ouchi, T.Tomita, A.Horie, A.Yoshida, K.Takahashi, H.Nishida, K.Lassak, H.Taka, R.Mineki, T.Fujimura, S.Kosono, C.Nishiyama, R.Masui, S.Kuramitsu, S.V.Albers, T.Kuzuyama, M.Nishiyama.

ABSTRACT

LysW has been identified as a carrier protein in the lysine biosynthetic pathway that is active through the conversion of α-aminoadipate (AAA) to lysine. In this study, we found that the hyperthermophilic archaeon, Sulfolobus acidocaldarius, not only biosynthesizes lysine through LysW-mediated protection of AAA but also uses LysW to protect the amino group of glutamate in arginine biosynthesis. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions. The crystal structure of ArgX, the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW, was determined in complex with LysW. Structural comparison and enzymatic characterization using Sulfolobus LysX, Sulfolobus ArgX and Thermus LysX identify the amino acid motif responsible for substrate discrimination between AAA and glutamate. Phylogenetic analysis reveals that gene duplication events at different stages of evolution led to ArgX and LysX.