1BIX | pdb_00001bix

THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL DEOXYRIBOSE AT DNA ABASIC SITES

• PDB DOI: https://doi.org/10.2210/pdb1BIX/pdb

• Classification: DNA REPAIR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-06-19 Released: 1999-06-22 
• Deposition Author(s): Gorman, M.A., Morera, S., Rothwell, D.G., De La Fortelle, E., Mol, C.D., Tainer, J.A., Hickson, I.D., Freemont, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.269 (Depositor) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites.

Gorman, M.A., Morera, S., Rothwell, D.G., de La Fortelle, E., Mol, C.D., Tainer, J.A., Hickson, I.D., Freemont, P.S.

(1997) EMBO J 16: 6548-6558

• PubMed: 9351835 
• DOI: https://doi.org/10.1093/emboj/16.21.6548
• Primary Citation Related Structures: 
  1BIX


• PubMed Abstract: 
  

  The structure of the major human apurinic/ apyrimidinic endonuclease (HAP1) has been solved at 2.2 A resolution. The enzyme consists of two symmetrically related domains of similar topology and has significant structural similarity to both bovine DNase I and its Escherichia coli homologue exonuclease III (EXOIII). A structural comparison of these enzymes reveals three loop regions specific to HAP1 and EXOIII. These loop regions apparently act in DNA abasic site (AP) recognition and cleavage since DNase I, which lacks these loops, correspondingly lacks AP site specificity. The HAP1 structure furthermore suggests a mechanism for AP site binding which involves the recognition of the deoxyribose moiety in an extrahelical conformation, rather than a 'flipped-out' base opposite the AP site.

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Organizational Affiliation: 
• Protein Structure Laboratory, Imperial Cancer Research Fund, London, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.08 kDa 
• Atom Count: 2,350 
• Modeled Residue Count: 275 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP ENDONUCLEASE 1	A	287	Homo sapiens	Mutation(s): 0  EC: 4.2.99.18 (PDB Primary Data), 3.1.21 (UniProt), 3.1.11.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27695 (Homo sapiens) Explore P27695  Go to UniProtKB:  P27695
PHAROS:  P27695 GTEx:  ENSG00000100823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	F [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
SM	B [auth A], C [auth A], D [auth A], E [auth A]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.269 (Depositor) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.26	α = 90
b = 44.701	β = 103.45
c = 78.778	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOSFLM	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-22 
Deposition Author(s): Gorman, M.A., Morera, S., Rothwell, D.G., De La Fortelle, E., Mol, C.D., Tainer, J.A., Hickson, I.D., Freemont, P.S.

Revision History  

• Version 1.0: 1999-06-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations