4V1U

Heterocyclase in complex with substrate and Cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.E.Jaspars, M.Naismith, J.H.

(2015) Nat.Chem.Biol. 11: 558

  • DOI: 10.1038/nchembio.1841
  • Primary Citation of Related Structures:  

  • 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 cystei ...

    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

    BSRC, University of St Andrews, St Andrews, KY16 9RH.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYND
A, B
775Lyngbya sp. (strain PCC 8106)Mutation(s): 0 
Find proteins for A0YXD2 (Lyngbya sp. (strain PCC 8106))
Go to UniProtKB:  A0YXD2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PATE
C, D
64uncultured Prochloron spMutation(s): 0 
Gene Names: patE
Find proteins for A0MHA3 (uncultured Prochloron sp)
Go to UniProtKB:  A0MHA3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.800α = 90.00
b = 152.810β = 90.00
c = 182.840γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references
  • Version 1.2: 2015-07-01
    Type: Database references
  • Version 1.3: 2015-08-05
    Type: Database references