6NVO | pdb_00006nvo

Crystal structure of Pseudomonas putida nuclease MPE

• PDB DOI: https://doi.org/10.2210/pdb6NVO/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-02-05 Released: 2019-03-27 
• Deposition Author(s): Goldgur, Y., Shuman, S., Ejaz, A.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.263 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Activity and structure ofPseudomonas putidaMPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster.

Ejaz, A., Goldgur, Y., Shuman, S.

(2019) J Biological Chem 294: 7931-7941

• PubMed: 30894417 
• DOI: https://doi.org/10.1074/jbc.RA119.008049
• Primary Citation Related Structures: 
  6NVO, 6NVP


• PubMed Abstract: 
  

  A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are as follows: MPE, a DNA endonuclease; Lhr-Core, a 3'-5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-β-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here, we report that the Pseudomonas putida MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 Å resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp ³³ , His ³⁵ , Asp ⁷⁸ , Asn ¹¹² , His ¹²⁴ , His ¹⁴⁶ , and His ¹⁵⁸ A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the β sandwich that comprises the core of the metallophosphoesterase fold differs in MPE vis-à-vis Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily.

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Organizational Affiliation: 
• From the Molecular Biology and.
Structural Biology Programs, Sloan Kettering Institute, New York, New York 10065.
From the Molecular Biology and [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.42 kDa 
• Atom Count: 1,639 
• Modeled Residue Count: 200 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease MPE	A	216	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: PP_1102
UniProt
Find proteins for Q88NV2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88NV2  Go to UniProtKB:  Q88NV2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.263 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.224	α = 90
b = 72.995	β = 90
c = 41.748	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Goldgur, Y., Shuman, S., Ejaz, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R35 GM126945

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-05-29
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description