6TCX

Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway.

Juettner, N.E.Bogen, J.P.Bauer, T.A.Knapp, S.Pfeifer, F.Huettenhain, S.H.Meusinger, R.Kraemer, A.Fuchsbauer, H.L.

(2020) J Nat Prod 83: 2983-2995

  • DOI: https://doi.org/10.1021/acs.jnatprod.0c00201
  • Primary Citation of Related Structures:  
    6TCX

  • PubMed Abstract: 

    Streptomyces mobaraensis produces the papain inhibitor SPI consisting of a 12 kDa protein and small active compounds (SPI ac ). Purification of the papain inhibitory compounds resulted in four diverse chymostatin derivatives that were characterized by NMR and MS analysis. Chymostatins are hydrophobic tetrapeptide aldehydes from streptomycetes, e.g., S. lavendulae and S. hygroscopicus , that reverse chymosin-mediated angiotensin activation and inhibit other serine and cysteine proteases. Chymotrypsin and papain were both inhibited by the SPI ac compounds in the low nanomolar range. SPI ac differs from the characterized chymostatins by the exchange of phenylalanine for tyrosine. The crystal structure of one of these chymostatin variants confirmed its molecular structure and revealed a S-configured hemithioacetal bond with the catalytic Cys25 thiolate as well as close interactions with hydrophobic S1 and S2 subsite amino acids. A model for chymostatin biosynthesis is provided based on the discovery of clustered genes encoding several putative nonribosomal peptide synthetases; among them, there is the unusual CstF enzyme that accommodates two canonical amino acid activation domains as well as three peptide carrier protein domains.


  • Organizational Affiliation

    The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PapainA [auth AAA]212Carica papayaMutation(s): 0 
EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya)
Explore P00784 
Go to UniProtKB:  P00784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00784
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N1W (Subject of Investigation/LOI)
Query on N1W

Download Ideal Coordinates CCD File 
C [auth AAA](2~{R})-2-[[(1~{S})-1-[(6~{S})-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-[[(2~{S})-3-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]amino]-2-oxidanylidene-ethyl]carbamoylamino]-3-(4-hydroxyphenyl)propanoic acid
C30 H41 N7 O7
JRKYEAYRXQTOFS-JRBASJLZSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
B [auth AAA]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.644α = 90
b = 48.921β = 90
c = 101.547γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoXDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description