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PDBsum entry 2a8y

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2a8y
Jmol
Contents
Protein chains
(+ 6 more) 263 a.a. *
Ligands
SO4 ×24
MTA ×12
Waters ×3405
* Residue conservation analysis
PDB id:
2a8y
Name: Transferase
Title: Crystal structure of 5'-deoxy-5'methylthioadenosine phosphorylase complexed with 5'-deoxy- 5'methylthioadenosine and sulfate
Structure: 5'-methylthioadenosine phosphorylase (mtap). Chain: a, b, c, d, e, f, g, h, i, j, k, l. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Gene: ssmtapii. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
1.45Å     R-factor:   0.182     R-free:   0.202
Authors: Y.Zhang,M.Porcelli,G.Cacciapuoti,S.E.Ealick
Key ref:
Y.Zhang et al. (2006). The crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus, a thermophilic enzyme stabilized by intramolecular disulfide bonds. J Mol Biol, 357, 252-262. PubMed id: 16414070 DOI: 10.1016/j.jmb.2005.12.040
Date:
10-Jul-05     Release date:   28-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q97W94  (MTAP_SULSO) -  S-methyl-5'-thioadenosine phosphorylase
Seq:
Struc:
270 a.a.
263 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.28  - S-methyl-5'-thioadenosine phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha- D-ribose 1-phosphate
S-methyl-5'-thioadenosine
Bound ligand (Het Group name = MTA)
corresponds exactly
+ phosphate
= adenine
+ S-methyl-5-thio-alpha- D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleoside metabolic process   3 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.12.040 J Mol Biol 357:252-262 (2006)
PubMed id: 16414070  
 
 
The crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus, a thermophilic enzyme stabilized by intramolecular disulfide bonds.
Y.Zhang, M.Porcelli, G.Cacciapuoti, S.E.Ealick.
 
  ABSTRACT  
 
The crystal structure of Sulfolobus solfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II (SsMTAPII) in complex with 5'-deoxy-5'-methylthioadenosine (MTA) and sulfate was determined to 1.45A resolution. The hexameric structure of SsMTAPII is a dimer-of-trimers with one active site per monomer. The oligomeric assembly of the trimer and the monomer topology of SsMTAPII are almost identical with trimeric human 5'-deoxy-5'-methylthioadenosine phosphorylase (hMTAP). SsMTAPII is the first reported hexameric member in the trimeric class of purine nucleoside phosphorylase (PNP) from Archaea. Unlike hMTAP, which is highly specific for MTA, SsMTAPII also accepts adenosine as a substrate. The residues at the active sites of SsMTAPII and hMTAP are almost identical. The broad substrate specificity of SsMTAPII may be due to the flexibility of the C-terminal loop. SsMTAPII is extremely thermoactive and thermostable. The three-dimensional structure of SsMTAPII suggests that the unique dimer-of-trimers quaternary structure, a CXC motif at the C terminus, and two pairs of intrasubunit disulfide bridges may play an important role in its thermal stability.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of the SsMTAPII subunit. (a) A ribbon diagram representing the secondary structural elements in the SsMTAPII subunit (a helices, blue; b strands, green). The substrate MTA and sulfate are shown in ball-and-stick representation. The disordered loop composed of residues 255-261 is shown as a dotted line. (b) Topology diagram. The a helices are shown as blue rectangles, and the b strands are shown as green arrows. Each secondary structural element is labeled in its center with its designator and with its beginning and ending sequence number.
Figure 5.
Figure 5. Schematic representation of the SsMTAPII active site. Residues of SsMTAPII are shown in black boxes. Residues in red boxes identify structurally equivalent residues in human MTAP. Residues in blue boxes represent structurally equivalent residues in human PNP. An asterisk designates residues from the neighboring subunit. Key hydrogen bonds are indicated by broken lines with the corresponding donor-acceptor distance labeled.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 252-262) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19740110 G.Cacciapuoti, I.Peluso, F.Fuccio, and M.Porcelli (2009).
Purine nucleoside phosphorylases from hyperthermophilic Archaea require a CXC motif for stability and folding.
  FEBS J, 276, 5799-5805.  
18355316 M.Porcelli, L.Concilio, I.Peluso, A.Marabotti, A.Facchiano, and G.Cacciapuoti (2008).
Pyrimidine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus--biochemical characterization and homology modeling.
  FEBS J, 275, 1900-1914.  
18094473 P.H.Zwart, R.W.Grosse-Kunstleve, A.A.Lebedev, G.N.Murshudov, and P.D.Adams (2008).
Surprises and pitfalls arising from (pseudo)symmetry.
  Acta Crystallogr D Biol Crystallogr, 64, 99.  
17419725 G.Cacciapuoti, S.Gorassini, M.F.Mazzeo, R.A.Siciliano, V.Carbone, V.Zappia, and M.Porcelli (2007).
Biochemical and structural characterization of mammalian-like purine nucleoside phosphorylase from the Archaeon Pyrococcus furiosus.
  FEBS J, 274, 2482-2495.  
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.