4V1T

Heterocyclase in complex with substrate and Cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Analysis of Leader Peptide Binding Enables Leader-Free Cyanobactin Processing

Koehnke, J.Mann, G.Bent, A.F.Ludewig, H.Shirran, S.Botting, C.Lebl, T.Houssen, W.Jaspars, M.Naismith, J.H.

(2015) Nat Chem Biol 11: 558

  • DOI: 10.1038/nchembio.1841
  • Primary Citation of Related Structures:  
    4V1T, 4V1U, 4V1V

  • PubMed Abstract: 
  • Regioselective modification of amino acids within the context of a peptide is common to a number of biosynthetic pathways, and many of the resulting products have potential as therapeutics. The ATP-dependent enzyme LynD heterocyclizes multiple cysteine residues to thiazolines within a peptide substrate ...

    Regioselective modification of amino acids within the context of a peptide is common to a number of biosynthetic pathways, and many of the resulting products have potential as therapeutics. The ATP-dependent enzyme LynD heterocyclizes multiple cysteine residues to thiazolines within a peptide substrate. The enzyme requires the substrate to have a conserved N-terminal leader for full activity. Catalysis is almost insensitive to immediately flanking residues in the substrate, suggesting that recognition occurs distant from the active site. Nucleotide and peptide substrate co-complex structures of LynD reveal that the substrate leader peptide binds to and extends the β-sheet of a conserved domain of LynD, whereas catalysis is accomplished in another conserved domain. The spatial segregation of catalysis from recognition combines seemingly contradictory properties of regioselectivity and promiscuity, and it appears to be a conserved strategy in other peptide-modifying enzymes. A variant of LynD that efficiently processes substrates without a leader peptide has been engineered.


    Organizational Affiliation

    State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYNDA, B775Lyngbya aestuariiMutation(s): 0 
Find proteins for A0YXD2 (Lyngbya sp. (strain PCC 8106))
Explore A0YXD2 
Go to UniProtKB:  A0YXD2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PATEC, D64uncultured Prochloron sp.Mutation(s): 0 
Gene Names: patE
Find proteins for A0MHA3 (uncultured Prochloron sp)
Explore A0MHA3 
Go to UniProtKB:  A0MHA3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.76α = 90
b = 116.15β = 90
c = 183.54γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2015-07-01
    Changes: Database references
  • Version 1.3: 2015-08-05
    Changes: Database references
  • Version 1.4: 2017-09-13
    Changes: Data collection
  • Version 1.5: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations