Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant-L-Ala

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Structural insights into the substrate-bound condensation domains of non-ribosomal peptide synthetase AmbB.

Chu Yuan Kee, M.J.Bharath, S.R.Wee, S.Bowler, M.W.Gunaratne, J.Pan, S.Zhang, L.Song, H.

(2022) Sci Rep 12: 5353-5353

  • DOI: https://doi.org/10.1038/s41598-022-09188-8
  • Primary Citation of Related Structures:  
    7X0E, 7X0F, 7X17

  • PubMed Abstract: 

    Non-ribosomal peptide synthetases (NRPS) are multi-modular/domain enzymes that catalyze the synthesis of bioactive peptides. A crucial step in the process is peptide elongation accomplished by the condensation (C) domain with the aid of a peptidyl carrier or thiolation (T) domain. Here, we examined condensation reaction carried out by NRPS AmbB involved in biosynthesis of L-2-amino-4-methoxy-trans-3-butenoic acid (AMB) in P. aeruginosa. We determined crystal structures of the truncated T-C bidomain of AmbB in three forms, the apo enzyme with disordered T domain, the holo form with serine linked phosphopantetheine (Ppant) and a holo form with substrate (L-alanine) loaded onto Ppant. The two holo forms feature the T domain in a substrate-donation conformation. Mutagenesis combined with functional assays identified residues essential for the attachment of Ppant, anchoring the Ppant-L-Ala in the donor catalytic channel and the role of the conserved His953 in condensation activity. Altogether, these results provide structural insights into the condensation reaction at the donor site with a substrate-bound C domain of AmbB and lay the foundation for understanding the molecular mechanism of condensation which is crucial for AMB synthesis.

  • Organizational Affiliation

    Institute of Molecular and Cell Biology, 61 Biopolis drive, Singapore, 138673, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMB antimetabolite synthase AmbB
A, B, C, D
523Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ambBPA2305
Find proteins for Q9I1H0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I1H0 
Go to UniProtKB:  Q9I1H0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I1H0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.498α = 90
b = 71.61β = 110.14
c = 173.757γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description