1G8G

ATP SULFURYLASE FROM S. CEREVISIAE: THE BINARY PRODUCT COMPLEX WITH APS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation.

Ullrich, T.C.Blaesse, M.Huber, R.

(2001) EMBO J 20: 316-329

  • DOI: 10.1093/emboj/20.3.316
  • Primary Citation of Related Structures:  
    1G8H, 1G8G, 1G8F

  • PubMed Abstract: 
  • ATP sulfurylases (ATPSs) are ubiquitous enzymes that catalyse the primary step of intracellular sulfate activation: the reaction of inorganic sulfate with ATP to form adenosine-5'-phosphosulfate (APS) and pyrophosphate (PPi). With the crystal structure of ATPS from the yeast Saccharomyces cerevisiae, we have solved the first structure of a member of the ATP sulfurylase family ...

    ATP sulfurylases (ATPSs) are ubiquitous enzymes that catalyse the primary step of intracellular sulfate activation: the reaction of inorganic sulfate with ATP to form adenosine-5'-phosphosulfate (APS) and pyrophosphate (PPi). With the crystal structure of ATPS from the yeast Saccharomyces cerevisiae, we have solved the first structure of a member of the ATP sulfurylase family. We have analysed the crystal structure of the native enzyme at 1.95 Angstroms resolution using multiple isomorphous replacement (MIR) and, subsequently, the ternary enzyme product complex with APS and PPi bound to the active site. The enzyme consists of six identical subunits arranged in two stacked rings in a D:3 symmetric assembly. Nucleotide binding causes significant conformational changes, which lead to a rigid body structural displacement of domains III and IV of the ATPS monomer. Despite having similar folds and active site design, examination of the active site of ATPS and comparison with known structures of related nucleotidylyl transferases reveal a novel ATP binding mode that is peculiar to ATP sulfurylases.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. tullrich@biochem.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SULFATE ADENYLYLTRANSFERASEA, B511Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.4
UniProt
Find proteins for P08536 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P08536 
Go to UniProtKB:  P08536
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADX (Subject of Investigation/LOI)
Query on ADX

Download Ideal Coordinates CCD File 
RA [auth B], S [auth A]ADENOSINE-5'-PHOSPHOSULFATE
C10 H14 N5 O10 P S
IRLPACMLTUPBCL-KQYNXXCUSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
SA [auth B], T [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A] , CA [auth B] , D [auth A] , DA [auth B] , E [auth A] , EA [auth B] , F [auth A] , FA [auth B] , 
C [auth A],  CA [auth B],  D [auth A],  DA [auth B],  E [auth A],  EA [auth B],  F [auth A],  FA [auth B],  G [auth A],  GA [auth B],  O [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
AA [auth A] , BA [auth A] , TA [auth B] , U [auth A] , UA [auth B] , V [auth A] , VA [auth B] , W [auth A] , 
AA [auth A],  BA [auth A],  TA [auth B],  U [auth A],  UA [auth B],  V [auth A],  VA [auth B],  W [auth A],  WA [auth B],  X [auth A],  XA [auth B],  Y [auth A],  YA [auth B],  Z [auth A],  ZA [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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H [auth A], HA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth A], LA [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A] , IA [auth B] , M [auth A] , MA [auth B] , N [auth A] , NA [auth B] , OA [auth B] , P [auth A] , 
I [auth A],  IA [auth B],  M [auth A],  MA [auth B],  N [auth A],  NA [auth B],  OA [auth B],  P [auth A],  PA [auth B],  Q [auth A],  QA [auth B],  R [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.922α = 90
b = 185.922β = 90
c = 223.674γ = 120
Software Package:
Software NamePurpose
CCP4model building
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance