7QST

Crystal structure of homing endonuclease-associated PhoVMA intein (C1A)

• PDB DOI: https://doi.org/10.2210/pdb7QST/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-01-14 Released: 2022-03-30 
• Deposition Author(s): Beyer, H.M., Iwai, H.
• Funding Organization(s): Academy of Finland, Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.243 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins.

Beyer, H.M., Iwai, H.

(2022) Front Mol Biosci 9: 855511-855511

• PubMed: 35372505 
• DOI: https://doi.org/10.3389/fmolb.2022.855511
• Primary Citation of Related Structures:  
  7QSS, 7QST, 7QSU


• PubMed Abstract: 
  

  Inteins catalyze their removal from a host protein through protein splicing. Inteins that contain an additional site-specific endonuclease domain display genetic mobility via a process termed "homing" and thereby act as selfish DNA elements. We elucidated the crystal structures of two archaeal inteins associated with an active or inactive homing endonuclease domain. This analysis illustrated structural diversity in the accessory domains (ACDs) associated with the homing endonuclease domain. To augment homing endonucleases with highly specific DNA cleaving activity using the intein scaffold, we engineered the ACDs and characterized their homing site recognition. Protein engineering of the ACDs in the inteins illuminated a possible strategy for how inteins could avoid their extinction but spread via the acquisition of a diverse accessory domain.

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Organizational Affiliation: 

Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

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: 42.98 kDa 
• Atom Count: 2,826 
• Modelled Residue Count: 361 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit A	A	379	Pyrococcus horikoshii	Mutation(s): 1  Gene Names: HA331_07965
UniProt
Find proteins for O57728 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57728  Go to UniProtKB:  O57728

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
NI	D [auth A], E [auth A], F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.243 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.08	α = 90
b = 81.87	β = 112.85
c = 67.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Beyer, H.M., Iwai, H.

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Funding Organization	Location	Grant Number
Academy of Finland	Denmark	137995, 277335
Novo Nordisk Foundation	Denmark	NNF17OC0025402, NNF17OC0027550

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2022-04-06
  Changes: Data collection, Structure summary
• Version 1.2: 2022-04-13
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description