3NZM | pdb_00003nzm

Crystal structure of DNAE intein with N-extein in redox trap

• PDB DOI: https://doi.org/10.2210/pdb3NZM/pdb

• Classification: TRANSFERASE
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-07-16 Released: 2011-06-01 
• Deposition Author(s): Van Roey, P., Belfort, M., Callahan, B.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structure of catalytically competent intein caught in a redox trap with functional and evolutionary implications.

Callahan, B.P., Topilina, N.I., Stanger, M.J., Van Roey, P., Belfort, M.

(2011) Nat Struct Mol Biol 18: 630-633

• PubMed: 21460844 
• DOI: https://doi.org/10.1038/nsmb.2041
• Primary Citation Related Structures: 
  3NZM


• PubMed Abstract: 
  

  Here we describe self-splicing proteins, called inteins, that function as redox-responsive switches in bacteria. Redox regulation was achieved by engineering a disulfide bond between the intein's catalytic cysteine and a cysteine in the flanking 'extein' sequence. This interaction was validated by an X-ray structure, which includes a transient splice junction. A natural analog of the designed system was identified in Pyrococcus abyssi, suggesting an unprecedented form of adaptive, post-translational regulation.

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Organizational Affiliation: 
• Wadsworth Center, New York State Department of Health, Albany, New York, USA.

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: 18.98 kDa 
• Atom Count: 1,512 
• Modeled Residue Count: 164 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit alpha	A	168	Synechocystis sp. PCC 6803	Mutation(s): 8  Gene Names: dnaE-N, slr0603, dnaE-C, sll1572 EC: 2.7.7.7
UniProt
Find proteins for P74750 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74750  Go to UniProtKB:  P74750

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.22	α = 90
b = 53.74	β = 90
c = 67.96	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Van Roey, P., Belfort, M., Callahan, B.P.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-06
  Changes: Structure summary