4L6A | pdb_00004l6a

Structure of human mitochondrial 5'(3')-deoxyribonucleotidase

• PDB DOI: https://doi.org/10.2210/pdb4L6A/pdb

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


• Deposited: 2013-06-12 Released: 2014-02-12 
• Deposition Author(s): Pachl, P., Brynda, J., Rezacova, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.154 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.

Pachl, P., Fabry, M., Rosenberg, I., Simak, O., Rezacova, P., Brynda, J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 461-470

• PubMed: 24531480 
• DOI: https://doi.org/10.1107/S1399004713030502
• Primary Citation Related Structures: 
  4L57, 4L6A


• PubMed Abstract: 
  

  The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.

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Organizational Affiliation: 
• Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.68 kDa 
• Atom Count: 2,117 
• Modeled Residue Count: 201 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, mitochondrial	A	202	Homo sapiens	Mutation(s): 0  Gene Names: DNT2, NT5M EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPB1 (Homo sapiens) Explore Q9NPB1  Go to UniProtKB:  Q9NPB1
PHAROS:  Q9NPB1 GTEx:  ENSG00000205309

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	M [auth A], N [auth A], O [auth A], P [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	Q [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.154 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.41	α = 90
b = 73.41	β = 90
c = 106.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Pachl, P., Brynda, J., Rezacova, P.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations