4IJX | pdb_00004ijx

Crystal structure of human Ap4A hydrolase E58A mutant complexed with DPO

• PDB DOI: https://doi.org/10.2210/pdb4IJX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-12-24 Released: 2013-03-20 
• Deposition Author(s): Ge, H., Chen, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of wild-type and mutant human Ap4A hydrolase.

Ge, H., Chen, X., Yang, W., Niu, L., Teng, M.

(2013) Biochem Biophys Res Commun 432: 16-21

• PubMed: 23384440 
• DOI: https://doi.org/10.1016/j.bbrc.2013.01.095
• Primary Citation of Related Structures:  
  3U53, 4ICK, 4IJX


• PubMed Abstract: 
  

  Ap4A hydrolase (asymmetrical diadenosine tetraphosphate hydrolase, EC 3.6.1.17), an enzyme involved in a number of biological processes, is characterized as cleaving the polyphosphate chain at the fourth phosphate from the bound adenosine moiety. This paper presents the crystal structure of wild-type and E58A mutant human Ap4A hydrolase. Similar to the canonical Nudix fold, human Ap4A hydrolase shows the common αβα-sandwich architecture. Interestingly, two sulfate ions and one diphosphate coordinated with some conserved residues were observed in the active cleft, which affords a better understanding of a possible mode of substrate binding.

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Organizational Affiliation: 

Institute of Health Sciences and Modern Experiment Technology Center, Anhui University, Hefei 230601, People's Republic of China. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.21 kDa 
• Atom Count: 2,537 
• Modelled Residue Count: 290 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]	A, B	155	Homo sapiens	Mutation(s): 1  Gene Names: NUDT2, APAH1 EC: 3.6.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P50583 (Homo sapiens) Explore P50583  Go to UniProtKB:  P50583
PHAROS:  P50583 GTEx:  ENSG00000164978

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPO	D [auth A]	DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J
PO4	F [auth B], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.369	α = 90
b = 72.369	β = 90
c = 133.379	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Ge, H., Chen, X.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description