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PDBsum entry 1odi

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1odi
Jmol
Contents
Protein chains
(+ 0 more) 234 a.a. *
Ligands
SO4 ×8
ADN ×6
Waters ×391
* Residue conservation analysis
PDB id:
1odi
Name: Transferase
Title: Purine nucleoside phosphorylase from thermus thermophilus
Structure: Purine nucleoside phosphorylase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8
Biol. unit: Hexamer (from PDB file)
Resolution:
2.4Å     R-factor:   0.176     R-free:   0.234
Authors: T.H.Tahirov,E.Inagaki,M.Miyano
Key ref:
T.H.Tahirov et al. (2004). Crystal structure of purine nucleoside phosphorylase from Thermus thermophilus. J Mol Biol, 337, 1149-1160. PubMed id: 15046984 DOI: 10.1016/j.jmb.2004.02.016
Date:
19-Feb-03     Release date:   27-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SID9  (Q5SID9_THET8) -  Purine nucleoside phosphorylase
Seq:
Struc:
235 a.a.
234 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleoside metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1016/j.jmb.2004.02.016 J Mol Biol 337:1149-1160 (2004)
PubMed id: 15046984  
 
 
Crystal structure of purine nucleoside phosphorylase from Thermus thermophilus.
T.H.Tahirov, E.Inagaki, N.Ohshima, T.Kitao, C.Kuroishi, Y.Ukita, K.Takio, M.Kobayashi, S.Kuramitsu, S.Yokoyama, M.Miyano.
 
  ABSTRACT  
 
The purine nucleoside phosphorylase from Thermus thermophilus crystallized in space group P4(3)2(1)2 with the unit cell dimensions a = 131.9 A and c = 169.9 A and one biologically active hexamer in the asymmetric unit. The structure was solved by the molecular replacement method and refined at a 1.9A resolution to an r(free) value of 20.8%. The crystals of the binary complex with sulfate ion and ternary complexes with sulfate and adenosine or guanosine were also prepared and their crystal structures were refined at 2.1A, 2.4A and 2.4A, respectively. The overall structure of the T.thermophilus enzyme is similar to the structures of hexameric enzymes from Escherichia coli and Sulfolobus solfataricus, but significant differences are observed in the purine base recognition site. A base recognizing aspartic acid, which is conserved among the hexameric purine nucleoside phosphorylases, is Asn204 in the T.thermophilus enzyme, which is reminiscent of the base recognizing asparagine in trimeric purine nucleoside phosphorylases. Isothermal titration calorimetry measurements indicate that both adenosine and guanosine bind the enzyme with nearly similar affinity. However, the functional assays show that as in trimeric PNPs, only the guanosine is a true substrate of the T.thermophilus enzyme. In the case of adenosine recognition, the Asn204 forms hydrogen bonds with N6 and N7 of the base. While in the case of guanosine recognition, the Asn204 is slightly shifted together with the beta(9)alpha(7) loop and predisposed to hydrogen bond formation with O6 of the base in the transition state. The obtained experimental data suggest that the catalytic properties of the T.thermophilus enzyme are reminiscent of the trimeric rather than hexameric purine nucleoside phosphorylases.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The overall view of TtPNP hexamer. The subunits are represented by ribbons and highlighted by different colors. Ball and stick models for sulfate ions and adenosines indicate the active site locations. The Figure was prepared using Molscript[37.] and Raster3D. [38.]
Figure 7.
Figure 7. Proposed catalytic mechanism for TtPNP (see the text for details).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 1149-1160) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19575810 A.Chaikuad, and R.L.Brady (2009).
Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases.
  BMC Struct Biol, 9, 42.
PDB codes: 3emv 3enz
16220545 A.Ababou, and J.E.Ladbury (2006).
Survey of the year 2004: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 19, 79-89.  
16131758 C.Schnick, M.A.Robien, A.M.Brzozowski, E.J.Dodson, G.N.Murshudov, L.Anderson, J.R.Luft, C.Mehlin, W.G.Hol, J.A.Brannigan, and A.J.Wilkinson (2005).
Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.
  Acta Crystallogr D Biol Crystallogr, 61, 1245-1254.
PDB codes: 1sq6 2bsx
  16511068 R.Grenha, V.M.Levdikov, M.J.Fogg, E.V.Blagova, J.A.Brannigan, A.J.Wilkinson, and K.S.Wilson (2005).
Structure of purine nucleoside phosphorylase (DeoD) from Bacillus anthracis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 459-462.
PDB code: 1xe3
16344484 X.Zhang, and T.C.Bruice (2005).
The proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction.
  Proc Natl Acad Sci U S A, 102, 18356-18360.  
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.