4L57

High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase

• PDB DOI: https://doi.org/10.2210/pdb4L57/pdb

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


• Deposited: 2013-06-10 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: 1.08 Å
• R-Value Free: 0.183 
• R-Value Work: 0.144 
• R-Value Observed: 0.144 

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 of 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.

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: 46.42 kDa 
• Atom Count: 3,845 
• Modelled Residue Count: 384 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, cytosolic type	A, B	195	Homo sapiens	Mutation(s): 0  Gene Names: DNT1, NT5C, UMPH2 EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCD5 (Homo sapiens) Explore Q8TCD5  Go to UniProtKB:  Q8TCD5
PHAROS:  Q8TCD5 GTEx:  ENSG00000125458

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.183 
• R-Value Work: 0.144 
• R-Value Observed: 0.144 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.128	α = 68.16
b = 46.493	β = 81.47
c = 61.409	γ = 75.28

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
SHELXL	refinement

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: 2014-03-19
  Changes: Refinement description
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations