4M54

The structure of the staphyloferrin B precursor biosynthetic enzyme SbnB bound to N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid and NADH

Summary for 4M54

• Entry DOI: 10.2210/pdb4m54/pdb
• Descriptor: Putative ornithine cyclodeaminase, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: siderophore, iron, l-2, 3-diaminopropionic acid synthesis, nad(p) binding rossmann fold, lyase-lyase inhibitor complex, lyase/lyase inhibitor
• Biological source: Staphylococcus aureus subsp. aureus
• Total number of polymer chains: 1
• Total formula weight: 39008.05

Authors

Kobylarz, M.J.,Murphy, M.E.P. (deposition date: 2013-08-07, release date: 2014-07-09, Last modification date: 2024-02-28)

Primary citation

Kobylarz, M.J.,Grigg, J.C.,Takayama, S.J.,Rai, D.K.,Heinrichs, D.E.,Murphy, M.E.
Synthesis of L-2,3-diaminopropionic acid, a siderophore and antibiotic precursor.
Chem.Biol., 21:379-388, 2014

PubMed Abstract: L-2,3-diaminopropionic acid (L-Dap) is an amino acid that is a precursor of antibiotics and staphyloferrin B a siderophore produced by Staphylococcus aureus. SbnA and SbnB are encoded by the staphyloferrin B biosynthetic gene cluster and are implicated in L-Dap biosynthesis. We demonstrate here that SbnA uses PLP and substrates O-phospho-L-serine and L-glutamate to produce a metabolite N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid (ACEGA). SbnB is shown to use NAD(+) to oxidatively hydrolyze ACEGA to yield α-ketoglutarate and L-Dap. Also, we describe crystal structures of SbnB in complex with NADH and ACEGA as well as with NAD(+) and α-ketoglutarate to reveal the residues required for substrate binding, oxidation, and hydrolysis. SbnA and SbnB contribute to the iron sparing response of S. aureus that enables staphyloferrin B biosynthesis in the absence of an active tricarboxylic acid cycle.

PubMed: 24485762
DOI: 10.1016/j.chembiol.2013.12.011

Experimental method

X-RAY DIFFRACTION (2.36 Å)