3N9D | pdb_00003n9d

Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain

• PDB DOI: https://doi.org/10.2210/pdb3N9D/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-28 Released: 2010-08-11 
• Deposition Author(s): Shuman, S., Nair, P., Smith, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily

Nair, P.A., Smith, P., Shuman, S.

(2010) Proc Natl Acad Sci U S A 107: 12822-12827

• PubMed: 20616014 
• DOI: https://doi.org/10.1073/pnas.1005830107
• Primary Citation of Related Structures:  
  3N9B, 3N9D


• PubMed Abstract: 
  

  The DNA ligase D (LigD) 3'-phosphoesterase (PE) module is a conserved component of the bacterial nonhomologous end-joining (NHEJ) apparatus that performs 3' end-healing reactions at DNA double-strand breaks. Here we report the 1.9 A crystal structure of Pseudomonas aeruginosa PE, which reveals that PE exemplifies a unique class of DNA repair enzyme. PE has a distinctive fold in which an eight stranded beta barrel with a hydrophobic interior supports a crescent-shaped hydrophilic active site on its outer surface. Six essential side chains coordinate manganese and a sulfate mimetic of the scissile phosphate. The PE active site and mechanism are unique vis à vis other end-healing enzymes. We find PE homologs in archaeal and eukaryal proteomes, signifying that PEs comprise a DNA repair superfamily.

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Organizational Affiliation: 
• Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.9 kDa 
• Atom Count: 1,293 
• Modeled Residue Count: 148 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent DNA ligase	A	171	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: NP_250828.1, PA2138 EC: 6.5.1.1
UniProt
Find proteins for Q9I1X7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I1X7  Go to UniProtKB:  Q9I1X7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
YT3	E [auth A], F [auth A]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.997	α = 90
b = 56.585	β = 118.33
c = 43.503	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Shuman, S., Nair, P., Smith, P.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description