1M3H | pdb_00001m3h

Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide

• PDB DOI: https://doi.org/10.2210/pdb1M3H/pdb
• NAKB: 1M3H

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-06-27 Released: 2004-04-20 
• Deposition Author(s): Chung, S.J., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.282 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase

Chung, S.J., Verdine, G.L.

(2004) Chem Biol 11: 1643-1649

• PubMed: 15610848 
• DOI: https://doi.org/10.1016/j.chembiol.2004.09.014
• Primary Citation Related Structures: 
  1M3H, 1M3Q


• PubMed Abstract: 
  

  DNA glycosylase/lyases initiate the repair of damaged nucleobases in the genome by catalyzing excision of aberrant nucleobases and nicking of the lesion-containing DNA strand. Nearly all of these proteins have the unusual property of remaining tightly bound in vitro to the end products of the reaction cascade. We have taken advantage of this property to crystallize and structurally characterize the end product resulting from complete DNA processing by a catalytically active mutant form of human 8-oxoguanine DNA glycosylase (D268E hOgg1). The resulting structure is consistent with the currently accepted catalytic mechanism for the protein. Unexpectedly, however, soaking of a nucleobase analog into the crystals results in religation of the DNA backbone in situ.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.69 kDa 
• Atom Count: 3,140 
• Modeled Residue Count: 344 
• Deposited Residue Count: 347 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
8-Oxoguanine DNA Glycosylase	D [auth A]	317	Homo sapiens	Mutation(s): 1  Gene Names: ogg1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15527 (Homo sapiens) Explore O15527  Go to UniProtKB:  O15527
PHAROS:  O15527 GTEx:  ENSG00000114026

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'	A [auth B]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*CP*GP*TP*CP*CP*AP*(DDX))-3'	B [auth C]	8	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*TP*CP*TP*AP*CP*C)-3'	C [auth D]	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.282 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.345	α = 90
b = 92.345	β = 90
c = 211.345	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-20 
Deposition Author(s): Chung, S.J., Verdine, G.L.

Revision History  

• Version 1.0: 2004-04-20
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection, Refinement description