3G23

Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution

3G23 の概要

• エントリーDOI: 10.2210/pdb3g23/pdb
• 分子名称: LD-carboxypeptidase A, SULFATE ION, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: flavodoxin-like fold, catalytic triad, merops s66 unassigned peptidases family, the swivelling beta/beta/alpha domain fold, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-2, hydrolase
• 由来する生物種: Novosphingobium aromaticivorans
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 61741.39

構造登録者

Joint Center for Structural Genomics (JCSG) (登録日: 2009-01-30, 公開日: 2009-02-10, 最終更新日: 2024-11-06)

主引用文献

Das, D.,Herve, M.,Elsliger, M.A.,Kadam, R.U.,Grant, J.C.,Chiu, H.J.,Knuth, M.W.,Klock, H.E.,Miller, M.D.,Godzik, A.,Lesley, S.A.,Deacon, A.M.,Mengin-Lecreulx, D.,Wilson, I.A.
Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling.
J.Bacteriol., 195:5555-5566, 2013

PubMed Abstract: Approximately 50% of cell wall peptidoglycan in Gram-negative bacteria is recycled with each generation. The primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are GlcNAc-MurNAc(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. This complex process involves ∼15 proteins, among which the cytoplasmic enzyme ld-carboxypeptidase A (LdcA) catabolizes the bond between the last two l- and d-amino acid residues in the tetrapeptide to form the tripeptide, which is then utilized as a substrate by murein peptide ligase (Mpl). LdcA has been proposed as an antibacterial target. The crystal structure of Novosphingobium aromaticivorans DSM 12444 LdcA (NaLdcA) was determined at 1.89-Å resolution. The enzyme was biochemically characterized and its interactions with the substrate modeled, identifying residues potentially involved in substrate binding. Unaccounted electron density at the dimer interface in the crystal suggested a potential site for disrupting protein-protein interactions should a dimer be required to perform its function in bacteria. Our analysis extends the identification of functional residues to several other homologs, which include enzymes from bacteria that are involved in hydrocarbon degradation and destruction of coral reefs. The NaLdcA crystal structure provides an alternate system for investigating the structure-function relationships of LdcA and increases the structural coverage of the protagonists in bacterial cell wall recycling.

PubMed: 24123814
DOI: 10.1128/JB.00900-13

実験手法

X-RAY DIFFRACTION (1.89 Å)