PDBsum entry 5ein

Oxidoreductase/biosynthetic protein

PDB id: 5ein

Contents

Protein chains

344 a.a.

54 a.a.

Ligands

NAP ×2

FMT ×23

Metals

_ZN

Waters ×553

PDB id:

5ein

Name:

Oxidoreductase/biosynthetic protein

Title:

Crystal structure of c148a mutant of lysy from thermus thermophilus in complex with NADP+ and lysw-gamma-aminoadipic acid

Structure:

N-acetyl-gamma-glutamyl-phosphate/n-acetyl-gamma- aminoadipyl-phosphate reductase. Chain: a, b. Synonym: agpr,n-acetyl-glutamate semialdehyde/n-acetyl-aminoadipate semialdehyde dehydrogenase,nagsa dehydrogenase. Engineered: yes. Mutation: yes. Alpha-aminoadipate carrier protein lysw. Chain: c.

Source:

Thermus thermophilus (strain hb27 / atcc baa- 163 / dsm 7039). Organism_taxid: 262724. Strain: hb27 / atcc baa-163 / dsm 7039. Gene: argc2, argc, lysy, tt_c1542. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: codonplus ril. Thermus thermophilus.

Resolution:

1.70Å R-factor: 0.173 R-free: 0.210

Authors:

T.Shimizu,T.Tomita,M.Nishiyama

Key ref:

T.Shimizu et al. (2016). Crystal Structure of the LysY·LysW Complex from Thermus thermophilus. J Biol Chem, 291, 9948-9959. PubMed id: 26966182 DOI: 10.1074/jbc.M115.707034

Date:

30-Oct-15 Release date: 23-Mar-16

Protein chains

O50146  (LYSY_THET2) -  [LysW]-L-2-aminoadipate 6-phosphate reductase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 344 a.a.

Struc: 344 a.a.*

Protein chain

Q9ZND7  (Q9ZND7_THETH) -  Alpha-aminoadipate carrier protein LysW from Thermus thermophilus

Seq: 54 a.a.

Struc: 54 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.1.2.1.103 - [amino-group carrier protein]-6-phospho-L-2-aminoadipate reductase.
• Reaction: [amino-group carrier protein]-C-terminal-N-(1-carboxy-5-oxopentan-1-yl)- L-glutamine + phosphate + NADP⁺ = [amino-group carrier protein]-C- terminal-N-(1-carboxy-5-phosphooxy-5-oxopentan-1-yl)-L-glutamine + NADPH + H⁺

[amino-group carrier protein]-C-terminal-N-(1-carboxy-5-oxopentan-1-yl)- L-glutamine + phosphate (Bound ligand (Het Group name = NAP) corresponds exactly) + NADP(+) = [amino-group carrier protein]-C- terminal-N-(1-carboxy-5-phosphooxy-5-oxopentan-1-yl)-L-glutamine + NADPH + H(+)

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

reference

DOI no: 10.1074/jbc.M115.707034

J Biol Chem 291:9948-9959 (2016)

PubMed id: 26966182

Crystal Structure of the LysY·LysW Complex from Thermus thermophilus.

T.Shimizu, T.Tomita, T.Kuzuyama, M.Nishiyama.

ABSTRACT

Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of α-aminoadipate (AAA). The resulting LysW-γ-AAA is phosphorylated by LysZ to form LysW-γ-AAA phosphate, which is subsequently reduced to LysW-γ-aminoadipic semialdehyde (LysW-γ-AASA) through a reaction catalyzed by LysY. In this study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-γ-AASA and TtLysW-γ-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively charged residues on helix α9 and the β11-α10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and TtLysW are important for the function of TtLysY. The extended LysW recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ·TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY.