1BNK

HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA

• PDB DOI: https://doi.org/10.2210/pdb1BNK/pdb
• NAKB: 1BNK

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-07-29 Released: 1998-10-21 
• Deposition Author(s): Lau, A.Y., Schaerer, O.D., Samson, L., Verdine, G.L., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.

Lau, A.Y., Scharer, O.D., Samson, L., Verdine, G.L., Ellenberger, T.

(1998) Cell 95: 249-258

• PubMed: 9790531 
• DOI: https://doi.org/10.1016/s0092-8674(00)81755-9
• Primary Citation of Related Structures:  
  1BNK


• PubMed Abstract: 
  

  DNA N-glycosylases are base excision-repair proteins that locate and cleave damaged bases from DNA as the first step in restoring the genetic blueprint. The human enzyme 3-methyladenine DNA glycosylase removes a diverse group of damaged bases from DNA, including cytotoxic and mutagenic alkylation adducts of purines. We report the crystal structure of human 3-methyladenine DNA glycosylase complexed to a mechanism-based pyrrolidine inhibitor. The enzyme has intercalated into the minor groove of DNA, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site, where a bound water is poised for nucleophilic attack. The structure shows an elegant means of exposing a nucleotide for base excision as well as a network of residues that could catalyze the in-line displacement of a damaged base from the phosphodeoxyribose backbone.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.86 kDa 
• Atom Count: 2,105 
• Modelled Residue Count: 226 
• Deposited Residue Count: 242 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (3-METHYLADENINE DNA GLYCOSYLASE)	C [auth A]	216	Homo sapiens	Mutation(s): 0  EC: 3.2.2.21
UniProt & NIH Common Fund Data Resources
Find proteins for P29372 (Homo sapiens) Explore P29372  Go to UniProtKB:  P29372
PHAROS:  P29372 GTEx:  ENSG00000103152

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*AP*TP*GP*YRRP*TP*TP*GP*CP*CP*T)-3')	A [auth D]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')	B [auth E]	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.75	α = 90
b = 57.1	β = 90
c = 128.45	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-21 
Deposition Author(s): Lau, A.Y., Schaerer, O.D., Samson, L., Verdine, G.L., Ellenberger, T.

Revision History  

• Version 1.0: 1998-10-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations