5WPR

Crystal structure HpiC1 in C2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis.

Newmister, S.A.Li, S.Garcia-Borras, M.Sanders, J.N.Yang, S.Lowell, A.N.Yu, F.Smith, J.L.Williams, R.M.Houk, K.N.Sherman, D.H.

(2018) Nat Chem Biol 14: 345-351

  • DOI: https://doi.org/10.1038/s41589-018-0003-x
  • Primary Citation of Related Structures:  
    5WPP, 5WPR, 5WPS, 5WPU, 6AL6, 6AL7, 6AL8

  • PubMed Abstract: 

    Hapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These complex metabolites are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps: a rare Cope rearrangement, 6-exo-trig cyclization, and electrophilic aromatic substitution. Here we report the structure of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U in vitro. The 1.5-Å structure revealed a dimeric assembly with two calcium ions per monomer and with the active sites located at the distal ends of the protein dimer. Mutational analysis and computational methods uncovered key residues for an acid-catalyzed [3,3]-sigmatropic rearrangement, as well as specific determinants that control the position of terminal electrophilic aromatic substitution, leading to a switch from hapalindole to fischerindole alkaloids.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
12-epi-hapalindole C/U synthase225Fischerella sp. ATCC 43239Mutation(s): 0 
Gene Names: hpiU5
UniProt
Find proteins for A0A076NBW8 (Fischerella sp. ATCC 43239)
Explore A0A076NBW8 
Go to UniProtKB:  A0A076NBW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A076NBW8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.846α = 90
b = 49.522β = 110.51
c = 53.135γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1205646
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA70375
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118101
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM076477
National Science Foundation (NSF, United States)United StatesOCI-1053575

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description