6TH7

Structure of porcine pancreatic elastase in complex with tutuilamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 4.0 of the entry. See complete history


Literature

Tutuilamides A-C: Vinyl-Chloride-Containing Cyclodepsipeptides from Marine Cyanobacteria with Potent Elastase Inhibitory Properties.

Keller, L.Canuto, K.M.Liu, C.Suzuki, B.M.Almaliti, J.Sikandar, A.Naman, C.B.Glukhov, E.Luo, D.Duggan, B.M.Luesch, H.Koehnke, J.O'Donoghue, A.J.Gerwick, W.H.

(2020) ACS Chem Biol 15: 751-757

  • DOI: https://doi.org/10.1021/acschembio.9b00992
  • Primary Citation of Related Structures:  
    6TH7

  • PubMed Abstract: 

    Marine cyanobacteria (blue-green algae) have been shown to possess an enormous capacity to produce structurally diverse natural products that exhibit a broad spectrum of potent biological activities, including cytotoxic, antifungal, antiparasitic, antiviral, and antibacterial activities. Using mass-spectrometry-guided fractionation together with molecular networking, cyanobacterial field collections from American Samoa and Palmyra Atoll yielded three new cyclic peptides, tutuilamides A-C. Their structures were established by spectroscopic techniques including 1D and 2D NMR, HR-MS, and chemical derivatization. Structure elucidation was facilitated by employing advanced NMR techniques including nonuniform sampling in combination with the 1,1-ADEQUATE experiment. These cyclic peptides are characterized by the presence of several unusual residues including 3-amino-6-hydroxy-2-piperidone and 2-amino-2-butenoic acid, together with a novel vinyl chloride-containing residue. Tutuilamides A-C show potent elastase inhibitory activity together with moderate potency in H-460 lung cancer cell cytotoxicity assays. The binding mode to elastase was analyzed by X-ray crystallography revealing a reversible binding mode similar to the natural product lyngbyastatin 7. The presence of an additional hydrogen bond with the amino acid backbone of the flexible side chain of tutuilamide A, compared to lyngbyastatin 7, facilitates its stabilization in the elastase binding pocket and possibly explains its enhanced inhibitory potency.


  • Organizational Affiliation

    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chymotrypsin-like elastase family member 1
A, B
240Sus scrofaMutation(s): 0 
EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa)
Explore P00772 
Go to UniProtKB:  P00772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00772
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tutuilamide9synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tutuilamide9synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
5XU
Query on 5XU
C
L-PEPTIDE LINKINGC3 H7 N OALA
AA4
Query on AA4
C
L-PEPTIDE LINKINGC5 H11 N O3ALA
ABA
Query on ABA
C
L-PEPTIDE LINKINGC4 H9 N O2ALA
PHA
Query on PHA
C
L-PEPTIDE LINKINGC9 H11 N OPHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.258α = 90
b = 99.114β = 90
c = 117.034γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKO4116_3_1

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 2.0: 2022-12-28
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.1: 2024-01-31
    Changes: Refinement description
  • Version 4.0: 2024-05-01
    Changes: Polymer sequence