7DQ5

Crystal structure of HitB in complex with (S)-beta-phenylalanine sulfamoyladenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mutational Biosynthesis of Hitachimycin Analogs Controlled by the beta-Amino Acid-Selective Adenylation Enzyme HitB.

Kudo, F.Takahashi, S.Miyanaga, A.Nakazawa, Y.Nishino, K.Hayakawa, Y.Kawamura, K.Ishikawa, F.Tanabe, G.Iwai, N.Nagumo, Y.Usui, T.Eguchi, T.

(2021) ACS Chem Biol 16: 539-547

  • DOI: https://doi.org/10.1021/acschembio.1c00003
  • Primary Citation of Related Structures:  
    7DQ5, 7DQ6

  • PubMed Abstract: 

    Hitachimycin is a macrolactam antibiotic with an ( S )-β-phenylalanine (β-Phe) at the starter position of its polyketide skeleton. ( S )-β-Phe is formed from l-α-phenylalanine by the phenylananine-2,3-aminomutase HitA in the hitachimycin biosynthetic pathway. In this study, we produced new hitachimycin analogs via mutasynthesis by feeding various ( S )-β-Phe analogs to a Δ hitA strain. We obtained six hitachimycin analogs with F at the ortho , meta , or para position and Cl, Br, or a CH 3 group at the meta position of the phenyl moiety, as well as two hitachimycin analogs with thienyl substitutions. Furthermore, we carried out a biochemical and structural analysis of HitB, a β-amino acid-selective adenylation enzyme that introduces ( S )-β-Phe into the hitachimycin biosynthetic pathway. The K M values of the incorporated ( S )-β-Phe analogs and natural ( S )-β-Phe were similar. However, the K M values of unincorporated ( S )-β-Phe analogs with Br and a CH 3 group at the ortho or para position of the phenyl moiety were high, indicating that HitB functions as a gatekeeper to select macrolactam starter units during mutasynthesis. The crystal structure of HitB in complex with ( S )-β-3-Br-phenylalanine sulfamoyladenosine (β- m -Br-Phe-SA) revealed that the bulky meta- Br group is accommodated by the conformational flexibility around Phe328, whose side chain is close to the meta position. The aromatic group of β- m -Br-Phe-SA is surrounded by hydrophobic and aromatic residues, which appears to confer the conformational flexibility that enables HitB to accommodate the meta -substituted ( S )-β-Phe. The new hitachimycin analogs exhibited different levels of biological activity in HeLa cells and multidrug-sensitive budding yeast, suggesting that they may target different molecules.


  • Organizational Affiliation

    Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo 152-8551, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ATP-dependent b-aminoacyl-ACP synthetase
A, B
549Embleya scabrisporaMutation(s): 0 
Gene Names: hitB
UniProt
Find proteins for A0A0F7R6G7 (Embleya scabrispora)
Explore A0A0F7R6G7 
Go to UniProtKB:  A0A0F7R6G7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7R6G7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.681α = 90
b = 93.639β = 90
c = 165.052γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description