4MUM

Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant

• PDB DOI: https://doi.org/10.2210/pdb4MUM/pdb

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


• Deposited: 2013-09-22 Released: 2014-02-26 
• Deposition Author(s): Pachl, P., Rezacova, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.149 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

Literature

Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase.

Pachl, P., Fabry, M., Veverka, V., Brynda, J., Rezacova, P.

(2015) J Enzyme Inhib Med Chem 30: 63-68

• PubMed: 24506201 
• DOI: https://doi.org/10.3109/14756366.2013.879577
• Primary Citation of Related Structures:  
  4MUM


• PubMed Abstract: 
  

  Human mitochondrial 5'(3')-deoxyribonucleotidase (mdN) catalyzes dephosphorylation of nucleoside monophosphates, and thus helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Mature mdN is a 23-kDa dimeric protein with highest expression levels in the heart, brain and skeletal muscle. We have identified an alternative splice variant of the mdN gene containing an 18-nucleotide insertion encoding 6 amino acids (GKWPAT) at the 3'-end of the penultimate exon 4. We recombinantly expressed this enzyme variant and characterized its biochemical and kinetic properties as well as its three-dimensional structure. Our high-resolution (1.27 Å) crystal structure revealed that the insertion forms a loop located in the vicinity of the active site pocket and affects enzyme kinetic parameters as well as protein thermal stability.

---

Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry and.

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: 25.23 kDa 
• Atom Count: 2,089 
• Modelled Residue Count: 198 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial 5' nucleotidase	A	207	Homo sapiens	Mutation(s): 0  Gene Names: DNT1, NT5C, UMPH2 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	N [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS	O [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	L [auth A], M [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]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.149 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.372	α = 90
b = 73.372	β = 90
c = 106.672	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Pachl, P., Rezacova, P.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description