PDBsum entry 6t3t

Lyase

PDB id: 6t3t

Contents

Protein chains

300 a.a.

Ligands

SO4 ×4

Waters ×751

PDB id:

6t3t

Name:

Lyase

Title:

Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph methylacidiphilum fumariolicum solv

Structure:

4-hydroxy-tetrahydrodipicolinate synthase. Chain: b, a, c, d. Synonym: htpa synthase. Ec: 4.3.3.7

Source:

Methylacidiphilum fumariolicum solv. Organism_taxid: 1156937

Resolution:

2.10Å R-factor: 0.184 R-free: 0.232

Authors:

R.Schmitz,A.Dietl,M.Mueller,T.Berben,H.Op Den Camp,T.Barends

Key ref:

R.A.Schmitz et al. (2020). Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway. Acta Crystallogr F Struct Biol Commun, 76, 199-208. PubMed id: 32356521 DOI: 10.1107/S2053230X20005294

Date:

11-Oct-19 Release date: 06-May-20

Protein chains

I0JZ23  (I0JZ23_METFB) -  4-hydroxy-tetrahydrodipicolinate synthase from Methylacidiphilum fumariolicum (strain SolV)

Seq: 301 a.a.

Struc: 300 a.a.

Enzyme reactions

• Enzyme class: E.C.4.3.3.7 - 4-hydroxy-tetrahydrodipicolinate synthase.
• Reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5- tetrahydrodipicolinate + H2O + H⁺

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

Added reference

DOI no: 10.1107/S2053230X20005294

Acta Crystallogr F Struct Biol Commun 76:199-208 (2020)

PubMed id: 32356521

Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway.

R.A.Schmitz, A.Dietl, M.Müller, T.Berben, H.J.M.Op den Camp, T.R.M.Barends.

ABSTRACT

The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and L-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.