3U53

Crystal structure of human Ap4A hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of wild-type and mutant human Ap4A hydrolase

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

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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Institute of Health Sciences and Modern Experiment Technology Center, Anhui University, Hefei 230601, People's Republic of China. hhge@ahu.edu.cn



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]A, B, C, D155Homo sapiensMutation(s): 0 
Gene Names: NUDT2APAH1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , M [auth C] , 
E [auth A],  F [auth A],  G [auth A],  I [auth B],  J [auth B],  K [auth B],  L [auth B],  M [auth C],  N [auth C],  O [auth C],  P [auth C],  Q [auth C],  R [auth D],  S [auth D],  T [auth D],  U [auth D],  V [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.485α = 90
b = 72.485β = 90
c = 133.491γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2011-10-10 
  • Released Date: 2012-10-10 
  • Deposition Author(s): Ge, H.H., Teng, M.K.

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references