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: 1.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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:  
    2PEZ, 2PEY

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPS synthetase 1) (PAPSS 1) (Sulfurylase kinase 1) (SK1) (SK 1)AB179Homo sapiensMutation(s): 0 
Gene Names: PAPSS1ATPSK1PAPSS
EC: 2.7.7.4 (UniProt), 2.7.1.25 (UniProt)
Find proteins for O43252 (Homo sapiens)
Explore O43252 
Go to UniProtKB:  O43252
NIH Common Fund Data Resources
PHAROS  O43252
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GGZ
Query on GGZ

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
DAT
Query on DAT

Download CCD File 
A, B
2'-DEOXYADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.09α = 90
b = 59.4β = 90
c = 139.02γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance