1HU0 | pdb_00001hu0

CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1HU0/pdb
• NAKB: 1HU0

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


• Deposited: 2001-01-03 Released: 2003-02-25 
• Deposition Author(s): Fromme, J.C., Bruner, S.D., Yang, W., Karplus, M., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.245 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Product-Assisted Catalysis in base-excision DNA Repair

Fromme, J.C., Bruner, S.D., Yang, W., Karplus, M., Verdine, G.L.

(2003) Nat Struct Biol 10: 204-211

• PubMed: 12592398 
• DOI: https://doi.org/10.1038/nsb902
• Primary Citation Related Structures: 
  1HU0, 1LWV, 1LWW, 1LWY


• PubMed Abstract: 
  

  Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their excision. How such proteins accomplish the feat of catalyzing no fewer than five sequential reaction steps using a single active site has been unknown. To help answer this, we report the structure of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine DNA glycosylase. This structure and supporting biochemical results reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, 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: 45.63 kDa 
• Atom Count: 3,200 
• Modeled Residue Count: 344 
• Deposited Residue Count: 354 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8-OXOGUANINE DNA GLYCOSYLASE 1	C [auth A]	324	Homo sapiens	Mutation(s): 0  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(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'	A [auth D]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3'	B [auth E]	15	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXG	E [auth A]	8-OXOGUANINE C5 H3 N5 O2 UBKVUFQGVWHZIR-UHFFFAOYSA-N
CA	D [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.245 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.988	α = 90
b = 91.988	β = 90
c = 211.615	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: 2003-02-25 
Deposition Author(s): Fromme, J.C., Bruner, S.D., Yang, W., Karplus, M., Verdine, G.L.

Revision History  

• Version 1.0: 2003-02-25
  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: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary