4B23 | pdb_00004b23

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

• PDB DOI: https://doi.org/10.2210/pdb4B23/pdb
• NAKB: 4B23

• Classification: HYDROLASE/DNA
• Organism(s): Schizosaccharomyces pombe, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-12 Released: 2013-01-09 
• Deposition Author(s): Dalhus, B., Nilsen, L., Korvald, H., Huffman, J., Forstrom, R.J., McMurray, C.T., Alseth, I., Tainer, J.A., Bjoras, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.290 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Literature

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2.

Dalhus, B., Nilsen, L., Korvald, H., Huffman, J., Forstrom, R.J., Mcmurray, C.T., Alseth, I., Tainer, J.A., Bjoras, M.

(2013) Structure 21: 154

• PubMed: 23245849 
• DOI: https://doi.org/10.1016/j.str.2012.11.004
• Primary Citation Related Structures: 
  4B21, 4B22, 4B23, 4B24


• PubMed Abstract: 
  

  Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which further pass on nicked DNA to downstream DNA polymerases and ligases. The coordinated handover of cytotoxic intermediates between different BER enzymes is most likely facilitated by the DNA conformation. Here, we present the atomic structure of Schizosaccharomyces pombe Mag2 in complex with DNA to reveal an unexpected structural basis for nonenzymatic AP site recognition with an unflipped AP site. Two surface-exposed loops intercalate and widen the DNA minor groove to generate a DNA conformation previously only found in the mismatch repair MutS-DNA complex. Consequently, the molecular role of Mag2 appears to be AP site recognition and protection, while possibly facilitating damage signaling by structurally sculpting the DNA substrate.

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Organizational Affiliation: 
• Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway.
Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway.
Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, Rochester, MN 55905, USA; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop: 83R0101, Berkeley, CA 94720, USA.
Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway. Electronic address: [e-mail].
Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Bioenergy/GTL and Structural Biology, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop: 83R0101, Berkeley, CA 94720, USA. Electronic address: [e-mail].
Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].

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: 32.96 kDa 
• Atom Count: 2,291 
• Modeled Residue Count: 229 
• Deposited Residue Count: 254 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAG2, DNA-3-METHYLADENINE GLYCOSYLASE 2	A	232	Schizosaccharomyces pombe	Mutation(s): 0  EC: 3.2.2.21
UniProt
Find proteins for O94468 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O94468  Go to UniProtKB:  O94468

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*AP*CP*(3DR)P*AP*AP*TP*CP*GP)-3'	B [auth X]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*TP*TP*GP*GP*TP*AP*GP*CP)-3'	C [auth Y]	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.290 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.48	α = 90
b = 84.52	β = 90
c = 125.75	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Dalhus, B., Nilsen, L., Korvald, H., Huffman, J., Forstrom, R.J., McMurray, C.T., Alseth, I., Tainer, J.A., Bjoras, M.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other