3H5R

Crystal structure of E. coli MccB + Succinimide

Summary for 3H5R

• Entry DOI: 10.2210/pdb3h5r/pdb
• Related: 3H5A 3H5N 3H9G 3H9J 3H9Q
• Related PRD ID: PRD_000183
• Descriptor: MccB protein, Microcin C7 analog, ZINC ION, ... (5 entities in total)
• Functional Keywords: ubiquitin-activating enzyme, microcin, bacteriocin, mcc7, peptide antibiotic, n-p bond formation, antibiotic, antimicrobial, phosphoprotein, transferase, transferase-antibiotic complex, transferase/antibiotic
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 161076.14

Authors

Regni, C.A.,Roush, R.F.,Miller, D.,Nourse, A.,Walsh, C.T.,Schulman, B.A. (deposition date: 2009-04-22, release date: 2009-06-16, Last modification date: 2024-10-16)

Primary citation

Regni, C.A.,Roush, R.F.,Miller, D.J.,Nourse, A.,Walsh, C.T.,Schulman, B.A.
How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic.
Embo J., 28:1953-1964, 2009

PubMed Abstract: The 39-kDa Escherichia coli enzyme MccB catalyses a remarkable posttranslational modification of the MccA heptapeptide during the biosynthesis of microcin C7 (MccC7), a 'Trojan horse' antibiotic. The approximately 260-residue C-terminal region of MccB is homologous to ubiquitin-like protein (UBL) activating enzyme (E1) adenylation domains. Accordingly, MccB-catalysed C-terminal MccA-acyl-adenylation is reminiscent of the E1-catalysed activation reaction. However, unlike E1 substrates, which are UBLs with a C-terminal di-glycine sequence, MccB's substrate, MccA, is a short peptide with an essential C-terminal Asn. Furthermore, after an intramolecular rearrangement of MccA-acyl-adenylate, MccB catalyses a second, unique reaction, producing a stable phosphoramidate-linked analogue of acyl-adenylated aspartic acid. We report six-crystal structures of MccB in apo, substrate-, intermediate-, and inhibitor-bound forms. Structural and kinetic analyses reveal a novel-peptide clamping mechanism for MccB binding to heptapeptide substrates and a dynamic-active site for catalysing dual adenosine triphosphate-consuming reactions. The results provide insight into how a distinctive member of the E1 superfamily carries out two-step activation for generating the peptidyl-antibiotic MccC7.

PubMed: 19494832
DOI: 10.1038/emboj.2009.146

Experimental method

X-RAY DIFFRACTION (2.1 Å)