1MOW | pdb_00001mow

E-DreI

• PDB DOI: https://doi.org/10.2210/pdb1MOW/pdb
• NAKB: 1MOW

• Classification: Hydrolase/DNA
• Organism(s): Desulfurococcus mucosus, Chlamydomonas reinhardtii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-09-10 Released: 2002-11-29 
• Deposition Author(s): Chevalier, B.S., Kortemme, T., Chadsey, M.S., Baker, D., Monnat Jr., R.J., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.215 (DCC) 

Starting Model: experimental

Literature

Design, Activity and Structure of a Highly Specific Artificial Endonuclease

Chevalier, B.S., Kortemme, T., Chadsey, M.S., Baker, D., Monnat Jr., R.J., Stoddard, B.L.

(2002) Mol Cell 10: 895-905

• PubMed: 12419232 
• DOI: https://doi.org/10.1016/s1097-2765(02)00690-1
• Primary Citation Related Structures: 
  1MOW


• PubMed Abstract: 
  

  We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-DmoI and I-CreI and creating a new 1400 A(2) protein interface between these domains. Protein engineering was accomplished by combining computational redesign and an in vivo protein-folding screen. The resulting enzyme, E-DreI (Engineered I-DmoI/I-CreI), binds a long chimeric DNA target site with nanomolar affinity, cleaving it precisely at a rate equivalent to its natural parents. The structure of an E-DreI/DNA complex demonstrates the accuracy of the protein interface redesign algorithm and reveals how catalytic function is maintained during the creation of the new endonuclease. These results indicate that it may be possible to generate novel highly specific DNA binding proteins from homing endonucleases.

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Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue N. A3-023, Seattle, WA 98109, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 179.36 kDa 
• Atom Count: 10,717 
• Modeled Residue Count: 1,147 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI	I [auth A], J [auth D], K [auth G], L [auth J]	260	Desulfurococcus mucosus, Chlamydomonas reinhardtii This entity is chimeric	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P05725 (Chlamydomonas reinhardtii) Explore P05725  Go to UniProtKB:  P05725
Find proteins for P21505 (Desulfurococcus mucosus) Explore P21505  Go to UniProtKB:  P21505
UniProt Groups	P05725P21505

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'	A [auth B], C [auth E], E [auth H], G [auth K]	23	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'	B [auth C], D [auth F], F [auth I], H [auth L]	23	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	JA [auth D], KA [auth D], LA [auth D], MA [auth D], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], M [auth B], N [auth B], NA [auth D], OA [auth D], P [auth E], PA [auth D], Q [auth F], QA [auth D], RA [auth D], SA [auth D], TA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	HA [auth D], IA [auth D], O [auth E], R [auth A], S [auth A], T [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.257 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.215 (DCC) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.76	α = 90
b = 131.76	β = 90
c = 120.91	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-29 
Deposition Author(s): Chevalier, B.S., Kortemme, T., Chadsey, M.S., Baker, D., Monnat Jr., R.J., Stoddard, B.L.

Revision History  

• Version 1.0: 2002-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description