4ZA1

Crystal Structure of NosA Involved in Nosiheptide Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based Mechanistic Insights into Terminal Amide Synthase in Nosiheptide-Represented Thiopeptides Biosynthesis

Liu, S.Guo, H.Zhang, T.Han, L.Yao, P.Zhang, Y.Rong, N.Yu, Y.Lan, W.Wang, C.Ding, J.Wang, R.Liu, W.Cao, C.

(2015) Sci Rep 5: 12744-12744

  • DOI: 10.1038/srep12744

  • PubMed Abstract: 
  • Nosiheptide is a parent compound of thiopeptide family that exhibit potent activities against various bacterial pathogens. Its C-terminal amide formation is catalyzed by NosA, which is an unusual strategy for maturating certain thiopeptides by proces ...

    Nosiheptide is a parent compound of thiopeptide family that exhibit potent activities against various bacterial pathogens. Its C-terminal amide formation is catalyzed by NosA, which is an unusual strategy for maturating certain thiopeptides by processing their precursor peptides featuring a serine extension. We here report the crystal structure of truncated NosA1-111 variant, revealing three key elements, including basic lysine 49 (K49), acidic glutamic acid 101 (E101) and flexible C-terminal loop NosA112-151, are crucial to the catalytic terminal amide formation in nosiheptide biosynthesis. The side-chain of residue K49 and the C-terminal loop fasten the substrate through hydrogen bonds and hydrophobic interactions. The side-chain of residue E101 enhances nucleophilic attack of H2O to the methyl imine intermediate, leading to Cα-N bond cleavage and nosiheptide maturation. The sequence alignment of NosA and its homologs NocA, PbtH, TpdK and BerI, and the enzymatic assay suggest that the mechanistic studies on NosA present an intriguing paradigm about how NosA family members function during thiopeptide biosynthesis.


    Organizational Affiliation

    State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NosA
A, B, C
151Streptomyces actuosusMutation(s): 0 
Gene Names: nosA
Find proteins for C6FX40 (Streptomyces actuosus)
Go to UniProtKB:  C6FX40
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download SDF File 
Download CCD File 
A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 143.371α = 90.00
b = 143.371β = 90.00
c = 143.371γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Other