3ZXX | pdb_00003zxx

Structure of self-cleaved protease domain of PatA

• PDB DOI: https://doi.org/10.2210/pdb3ZXX/pdb

• Classification: HYDROLASE
• Organism(s): Prochloron didemni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-16 Released: 2012-08-29 
• Deposition Author(s): Koehnke, J., Zollman, D., Vendome, J., Raab, A., Houssen, W.E., Smith, M.C., Jaspars, M., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.174 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

The Discovery of New Cyanobactins from Cyanothece Pcc 7425 Defines a New Signature for Processing of Patellamides.

Houssen, W.E., Koehnke, J., Zollman, D., Vendome, J., Raab, A., Smith, M.C., Naismith, J.H., Jaspars, M.

(2012) Chembiochem 13: 2683

• PubMed: 23169461 
• DOI: https://doi.org/10.1002/cbic.201200661
• Primary Citation Related Structures: 
  3ZXX, 3ZXY


• PubMed Abstract: 
  

  Cyanobactins, including patellamides, are a group of cyanobacterial post-translationally modified ribosomal cyclic peptides. The final product should in theory be predictable from the sequence of the precursor peptide and the associated tailoring enzymes. Understanding the mechanism and recognition requirements of these enzymes will allow their rational engineering. We have identified three new cyanobactins from a Cyanothece PCC 7425 culture subjected to a heat shock. One of these compounds revealed a novel signature signal for ThcA, the subtilisin-like serine protease that is homologous to the patellamide protease PatA. The crystal structure of the latter and modelling studies allow rationalisation of the recognition determinants for both enzymes, consistent with the ribosomal biosynthetic origin of the new compounds.

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Organizational Affiliation: 
• Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 32.37 kDa 
• Atom Count: 2,341 
• Modeled Residue Count: 265 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBTILISIN-LIKE PROTEIN	A	307	Prochloron didemni	Mutation(s): 0
UniProt
Find proteins for Q52QI9 (Prochloron didemni) Explore Q52QI9  Go to UniProtKB:  Q52QI9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.174 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.21	α = 90
b = 84.21	β = 90
c = 41.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Koehnke, J., Zollman, D., Vendome, J., Raab, A., Houssen, W.E., Smith, M.C., Jaspars, M., Naismith, J.H.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 1.2: 2013-01-16
  Changes: Database references
• Version 1.3: 2013-11-06
  Changes: Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary