8UO7 | pdb_00008uo7

Bovine trypsin in complex with deacetylated wild type microviridin J

• PDB DOI: https://doi.org/10.2210/pdb8UO7/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus, Microcystis aeruginosa MRC
• Mutation(s): No 


• Deposited: 2023-10-19 Released: 2024-02-14 
• Deposition Author(s): Chen, W., Bruner, S.D.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Alternative Linkage Chemistries in the Chemoenzymatic Synthesis of Microviridin-Based Cyclic Peptides.

Patel, K.P., Chen, W.T., Delbecq, L., Bruner, S.D.

(2024) Org Lett 26: 1138-1142

• PubMed: 38306609 
• DOI: https://doi.org/10.1021/acs.orglett.3c04045
• Primary Citation Related Structures: 
  8UO7, 8UTL


• PubMed Abstract: 
  

  Engineering biosynthetic pathways to ribosomally synthesized and post-translationally modified peptides (RiPPs) offers several advantages for both in vivo and in vitro applications. Here we probe the ability of peptide cyclases to generate trimacrocycle microviridin analogs with non-native cross-links. The results demonstrate that diverse chemistries are tolerated by macrocyclases in the ATP-grasp family and allow for the construction of unique cyclic peptide architectures that retain protease inhibition activity. In addition, cocomplex structures of analogs bound to a model protease were determined, illustrating how changes in functional groups maintain peptide conformation and target binding.

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Organizational Affiliation: 
• Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.25 kDa 
• Atom Count: 1,811 
• Modeled Residue Count: 235 
• Deposited Residue Count: 236 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Deacetylated wildtype microviridin J	B [auth C]	13	Microcystis aeruginosa MRC	Mutation(s): 0
UniProt
Find proteins for B2G3C8 (Microcystis aeruginosa MRC) Explore B2G3C8  Go to UniProtKB:  B2G3C8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002533	B [auth C]	Deacylated Microviridin J	Cyclic peptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.65	α = 90
b = 71.65	β = 90
c = 72.976	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Aimless	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Chen, W., Bruner, S.D.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Structure summary