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PDBsum entry 1g8h
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protein ligands metals links
Transferase PDB id
1g8h

 

 

 

 

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Contents
Protein chains
510 a.a. *
Ligands
ADX ×2
POP ×2
ACY ×15
Metals
_CD ×11
_CA ×6
_NA ×12
_MG ×2
Waters ×600
* Residue conservation analysis
PDB id:
1g8h
Name: Transferase
Title: Atp sulfurylase from s. Cerevisiae: the ternary product complex with aps and ppi
Structure: Sulfate adenylyltransferase. Chain: a, b. Other_details: complexed with adenosine-5'-phosphosulfate and pyrophosphate
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s288c-fy1679. Other_details: native purification out of yeast cells
Biol. unit: Hexamer (from PDB file)
Resolution:
2.80Å     R-factor:   0.194     R-free:   0.245
Authors: T.C.Ullrich,M.Blaesse,R.Huber
Key ref:
T.C.Ullrich et al. (2001). Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation. EMBO J, 20, 316-329. PubMed id: 11157739 DOI: 10.1093/emboj/20.3.316
Date:
17-Nov-00     Release date:   23-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P08536  (MET3_YEAST) -  Sulfate adenylyltransferase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		511 a.a.
510 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.4  - sulfate adenylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: sulfate + ATP + H+ = adenosine 5'-phosphosulfate + diphosphate
sulfate
 + ATP
 + H(+)
 =
adenosine 5'-phosphosulfate
Bound ligand (Het Group name = ADX)
corresponds exactly 		+
diphosphate
Bound ligand (Het Group name = POP)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1093/emboj/20.3.316 EMBO J 20:316-329 (2001)
PubMed id: 11157739  
 
 
Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation.
T.C.Ullrich, M.Blaesse, R.Huber.
 
  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. 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.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Active site residues of the apo-protomer liganded with sulfate at 1.95 Å (A), the binary enzyme product complex with APS at 2.6 Å (B), and the ternary product complex with an additional pyrophosphate at 2.8 Å (C). All atoms are shown with the final 2F[o] - F[c] electron density contoured at 1.0 . 		Figure 6.
Figure 6 Schematic drawing of the coordination of APS in the binding pocket, its hydrogen bonding and hydrophobic interactions with solvent molecules and the residues of ATPS. Bond distances are given in Å.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 316-329) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19191354 C.Bertonati, M.Punta, M.Fischer, G.Yachdav, F.Forouhar, W.Zhou, A.P.Kuzin, J.Seetharaman, M.Abashidze, T.A.Ramelot, M.A.Kennedy, J.R.Cort, A.Belachew, J.F.Hunt, L.Tong, G.T.Montelione, and B.Rost (2009).
Structural genomics reveals EVE as a new ASCH/PUA-related domain.
  Proteins, 75, 760-773.
PDB codes: 1zce 2eve 2g2x 2gbs
19067028 M.E.Bradley, J.S.Rest, W.H.Li, and N.B.Schwartz (2009).
Sulfate activation enzymes: phylogeny and association with pyrophosphatase.
  J Mol Evol, 68, 1.  
19770499 S.C.Gay, I.H.Segel, and A.J.Fisher (2009).
Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity.
  Acta Crystallogr D Biol Crystallogr, 65, 1021-1031.
PDB code: 3cr8
  18607083 O.Y.Gavel, A.V.Kladova, S.A.Bursakov, J.M.Dias, S.Texeira, V.L.Shnyrov, J.J.Moura, I.Moura, M.J.Romão, and J.Trincão (2008).
Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 593-595.  
18388974 T.Simonics, and A.Maráz (2008).
Cloning of the ATP sulphurylase gene of Schizosaccharomyces pombe by functional complementation.
  Can J Microbiol, 54, 71-74.  
16387658 J.D.Mougous, D.H.Lee, S.C.Hubbard, M.W.Schelle, D.J.Vocadlo, J.M.Berger, and C.R.Bertozzi (2006).
Molecular basis for G protein control of the prokaryotic ATP sulfurylase.
  Mol Cell, 21, 109-122.
PDB code: 1zun
16933356 M.W.Schelle, and C.R.Bertozzi (2006).
Sulfate metabolism in mycobacteria.
  Chembiochem, 7, 1516-1524.  
  16511295 T.Arakaki, I.Le Trong, E.Phizicky, E.Quartley, G.DeTitta, J.Luft, A.Lauricella, L.Anderson, O.Kalyuzhniy, E.Worthey, P.J.Myler, D.Kim, D.Baker, W.G.Hol, and E.A.Merritt (2006).
Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 175-179.
PDB code: 2ar1
15583009 B.D.Spiegelberg, J.Dela Cruz, T.H.Law, and J.D.York (2005).
Alteration of lithium pharmacology through manipulation of phosphoadenosine phosphate metabolism.
  J Biol Chem, 280, 5400-5405.  
16102596 D.Mendoza-Cózatl, H.Loza-Tavera, A.Hernández-Navarro, and R.Moreno-Sánchez (2005).
Sulfur assimilation and glutathione metabolism under cadmium stress in yeast, protists and plants.
  FEMS Microbiol Rev, 29, 653-671.  
16260766 W.Sun, X.Xu, M.Pavlova, A.M.Edwards, A.Joachimiak, A.Savchenko, and D.Christendat (2005).
The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii.
  Protein Sci, 14, 3121-3128.
PDB code: 2as0
14613928 E.Hanna, K.F.Ng, I.J.MacRae, C.J.Bley, A.J.Fisher, and I.H.Segel (2004).
Kinetic and stability properties of Penicillium chrysogenum ATP sulfurylase missing the C-terminal regulatory domain.
  J Biol Chem, 279, 4415-4424.  
14747722 S.Harjes, A.Scheidig, and P.Bayer (2004).
Expression, purification and crystallization of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1.
  Acta Crystallogr D Biol Crystallogr, 60, 350-352.  
12810729 V.Saridakis, and E.F.Pai (2003).
Mutational, structural, and kinetic studies of the ATP-binding site of Methanobacterium thermoautotrophicum nicotinamide mononucleotide adenylyltransferase.
  J Biol Chem, 278, 34356-34363.
PDB codes: 1m8f 1m8g 1m8j 1m8k
12925800 Y.Taguchi, J.Hoseki, Y.Kakuta, and K.Fukuyama (2003).
Overproduction, crystallization and preliminary X-ray diffraction analysis of probable ATP sulfurylase from Thermus thermophilus HB8.
  Acta Crystallogr D Biol Crystallogr, 59, 1645-1647.  
12426581 I.J.MacRae, I.H.Segel, and A.J.Fisher (2002).
Allosteric inhibition via R-state destabilization in ATP sulfurylase from Penicillium chrysogenum.
  Nat Struct Biol, 9, 945-949.
PDB code: 1m8p
11751893 S.Garavaglia, I.D'Angelo, M.Emanuelli, F.Carnevali, F.Pierella, G.Magni, and M.Rizzi (2002).
Structure of human NMN adenylyltransferase. A key nuclear enzyme for NAD homeostasis.
  J Biol Chem, 277, 8524-8530.
PDB code: 1kku
11389593 I.J.MacRae, I.H.Segel, and A.J.Fisher (2001).
Crystal structure of ATP sulfurylase from Penicillium chrysogenum: insights into the allosteric regulation of sulfate assimilation.
  Biochemistry, 40, 6795-6804.
PDB code: 1i2d
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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