Apo-structure of serine hydroxymethyltransferase (PbzB) involved in benzobactin biosynthesis in P. chlororaphis subsp. piscium DSM 21509

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

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This is version 1.4 of the entry. See complete history


Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate-Containing Natural Products in Diverse Bacteria.

Shi, Y.M.Crames, J.J.Czech, L.Bozhuyuk, K.A.J.Shi, Y.N.Hirschmann, M.Lamberth, S.Claus, P.Paczia, N.Ruckert, C.Kalinowski, J.Bange, G.Bode, H.B.

(2022) Angew Chem Int Ed Engl 61: e202206106-e202206106

  • DOI: https://doi.org/10.1002/anie.202206106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Benzoxazolinate is a rare bis-heterocyclic moiety that interacts with proteins and DNA and confers extraordinary bioactivities on natural products, such as C-1027. However, the biosynthetic gene responsible for the key cyclization step of benzoxazolinate remains unclear. Herein, we show a putative acyl AMP-ligase responsible for the last cyclization step. We used the enzyme as a probe for genome mining and discovered that the orphan benzobactin gene cluster in entomopathogenic bacteria prevails across Proteobacteria and Firmicutes. It turns out that Pseudomonas chlororaphis produces various benzobactins, whose biosynthesis is highlighted by a synergistic effect of two unclustered genes encoding enzymes on boosting benzobactin production; the formation of non-proteinogenic 2-hydroxymethylserine by a serine hydroxymethyltransferase; and the types I and II NRPS architecture for structural diversity. Our findings reveal the biosynthetic potential of a widespread benzobactin gene cluster.

  • Organizational Affiliation

    Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase
A, B
460Pseudomonas chlororaphis subsp. pisciumMutation(s): 0 
Gene Names: glyAC4K37_3196
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.4α = 90
b = 59.64β = 109.41
c = 112.12γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2022-12-21
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description