2PEZ

Crystal structrue of deletion mutant of APS-kinase domain of human PAPS-synthetase 1 in complex with cyclic PAPS and dADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural mechanism for substrate inhibition of the adenosine 5'-phosphosulfate kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 and its ramifications for enzyme regulation.

Sekulic, N.Konrad, M.Lavie, A.

(2007) J.Biol.Chem. 282: 22112-22121

  • DOI: 10.1074/jbc.M701713200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In mammals, the universal sulfuryl group donor molecule 3'-phosphoadenosine 5'-phosphosulfate (PAPS) is synthesized in two steps by a bifunctional enzyme called PAPS synthetase. The APS kinase domain of PAPS synthetase catalyzes the second step in wh ...

    In mammals, the universal sulfuryl group donor molecule 3'-phosphoadenosine 5'-phosphosulfate (PAPS) is synthesized in two steps by a bifunctional enzyme called PAPS synthetase. The APS kinase domain of PAPS synthetase catalyzes the second step in which APS, the product of the ATP-sulfurylase domain, is phosphorylated on its 3'-hydroxyl group to yield PAPS. The substrate APS acts as a strong uncompetitive inhibitor of the APS kinase reaction. We generated truncated and point mutants of the APS kinase domain that are active but devoid of substrate inhibition. Structural analysis of these mutant enzymes reveals the intrasubunit rearrangements that occur upon substrate binding. We also observe intersubunit rearrangements in this dimeric enzyme that result in asymmetry between the two monomers. Our work elucidates the structural elements required for the ability of the substrate APS to inhibit the reaction at micromolar concentrations. Because the ATP-sulfurylase domain of PAPS synthetase influences these elements in the APS kinase domain, we propose that this could be a communication mechanism between the two domains of the bifunctional enzyme.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)
A, B
179Homo sapiensMutation(s): 0 
Gene Names: PAPSS1 (ATPSK1, PAPSS)
Find proteins for O43252 (Homo sapiens)
Go to Gene View: PAPSS1
Go to UniProtKB:  O43252
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAT
Query on DAT

Download SDF File 
Download CCD File 
A, B
2'-DEOXYADENOSINE-5'-DIPHOSPHATE
DADP
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N
 Ligand Interaction
GGZ
Query on GGZ

Download SDF File 
Download CCD File 
A
(2S,3AR,4R,6R,6AR)-4-(6-AMINO-9H-PURIN-9-YL)-6-({[(R)-HYDROXY(SULFOOXY)PHOSPHORYL]OXY}METHYL)TETRAHYDROFURO[3,4-D][1,3,2]DIOXAPHOSPHOL-2-OL 2-OXIDE
C10 H13 N5 O12 P2 S
BOTWXJFMSRDLBQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.090α = 90.00
b = 59.400β = 90.00
c = 139.020γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-03 
  • Released Date: 2007-05-29 
  • Deposition Author(s): Sekulic, N., Lavie, A.

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance