PDBsum entry 1k9s

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Transferase PDB id
Protein chains
(+ 0 more) 237 a.a. *
PO4 ×6
FM2 ×3
FM1 ×3
Waters ×1238
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Purine nucleoside phosphorylase from e. Coli in complex with formycin a derivative and phosphate
Structure: Purine nucleoside phosphorylase. Chain: a, b, c, d, e, f. Ec:
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Hexamer (from PQS)
2.00Å     R-factor:   0.161     R-free:   0.184
Authors: G.Koellner,A.Bzowska,B.Wielgus-Kutrowska,M.Luic,T.Steiner, W.Saenger,J.Stepinski
Key ref:
G.Koellner et al. (2002). Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism. J Mol Biol, 315, 351-371. PubMed id: 11786017 DOI: 10.1006/jmbi.2001.5211
30-Oct-01     Release date:   28-Nov-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0ABP8  (DEOD_ECOLI) -  Purine nucleoside phosphorylase DeoD-type
239 a.a.
237 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
Bound ligand (Het Group name = FM1)
matches with 58.00% similarity
Bound ligand (Het Group name = PO4)
corresponds exactly
= purine
+ alpha-D-ribose 1-phosphate
Purine deoxynucleoside
+ phosphate
= purine
+ 2'-deoxy-alpha-D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     nucleobase-containing compound metabolic process   6 terms 
  Biochemical function     catalytic activity     6 terms  


DOI no: 10.1006/jmbi.2001.5211 J Mol Biol 315:351-371 (2002)
PubMed id: 11786017  
Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism.
G.Koellner, A.Bzowska, B.Wielgus-Kutrowska, M.Luić, T.Steiner, W.Saenger, J.Stepiński.
The crystal structure of the ternary complex of hexameric purine nucleoside phosphorylase (PNP) from Escherichia coli with formycin A derivatives and phosphate or sulphate ions is determined at 2.0 A resolution. The hexamer is found as a trimer of unsymmetric dimers, which are formed by pairs of monomers with active sites in different conformations. The conformational difference stems from a flexible helix (H8: 214-236), which is continuous in one conformer, and segmented in the other. With the continuous helix, the entry into the active site pocket is wide open, and the ligands are bound only loosely ("open" or "loose binding" conformation). By segmentation of the helix (H8: 214-219 and H8': 223-236, separated by a gamma-turn), the entry into the active site is partially closed, the pocket is narrowed and the ligands are bound much more tightly ("closed" or "tight binding" conformation). Furthermore, the side-chain of Arg217 is carried by the moving helix into the active site. This residue, conserved in all homologous PNPs, plays an important role in the proposed catalytic mechanism. In this mechanism, substrate binding takes place in the open, and and the catalytic action occurs in the closed conformation. Catalytic action involves protonation of the purine base at position N7 by the side-chain of Asp204, which is initially in the acid form. The proton transfer is triggered by the Arg217 side-chain which is moved by the conformation change into hydrogen bond distance to Asp204. The mechanism explains the broad specificity of E. coli PNP, which allows 6-amino as well as 6-oxo-nucleosides as substrates. The observation of two kinds of binding sites is fully in line with solution experiments which independently observe strong and weak binding sites for phosphate as well as for the nucleoside inhibitor.
  Selected figure(s)  
Figure 7.
Figure 7. Difference electron density representing the inhibitor molecules found in the active sites of the closed monomer A (left), and the open monomer D (right). The density in monomer A is modeled with the initially used 6-methylformycin A, whereas in monomer D, the electron density is incompatible with the 6-methyl form but suggests binding of N7-methylformycin A instead (difference density after omitting the inhibitor and consecutive refinement; drawn at the 3s-level with DINO).
Figure 8.
Figure 8. Sections of the base binding modes observed in the E. coli PNP complexed with 6-methylformycin A and phosphate/sulphate. (a) The open or loose-binding conformation of the active site (observed in monomers D, E and F) binding a hydrolysis product of 6-methylformycin A, N7-methylformycin A. (b) The closed or tight-binding conformation of the active site (observed in monomers A, B, and C) binding 6-methylformycin A; for the disordered side-chain of Asp204, conformation 1 is shown. For a full listing of hydrogen bond contacts, including those of the second conformer of Asp204, see Table 6. Drawn with MOLSCRIPT. [57]
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 315, 351-371) copyright 2002.  
  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
19388075 S.Afshar, M.R.Sawaya, and S.L.Morrison (2009).
Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine.
  Protein Sci, 18, 1107-1114.
PDB codes: 3gb9 3ggs
19500588 T.D.Gruber, M.J.Borrok, W.M.Westler, K.T.Forest, and L.L.Kiessling (2009).
Ligand binding and substrate discrimination by UDP-galactopyranose mutase.
  J Mol Biol, 391, 327-340.
PDB code: 3gf4
17639373 A.Modrak-Wójcik, A.Kirilenko, D.Shugar, and B.Kierdaszuk (2008).
Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP) of bacterial (E. coli) and mammalian (human) origin.
  Eur Biophys J, 37, 153-164.  
17223688 A.Rinaldo-Matthis, C.Wing, M.Ghanem, H.Deng, P.Wu, A.Gupta, P.C.Tyler, G.B.Evans, R.H.Furneaux, S.C.Almo, C.C.Wang, and V.L.Schramm (2007).
Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues.
  Biochemistry, 46, 659-668.
PDB codes: 2i4t 2isc
16751611 A.Modrak-Wójcik, K.Stepniak, V.Akoev, M.Zółkiewski, and A.Bzowska (2006).
Molecular architecture of E. coli purine nucleoside phosphorylase studied by analytical ultracentrifugation and CD spectroscopy.
  Protein Sci, 15, 1794-1800.  
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
15983408 W.Bu, E.C.Settembre, M.H.el Kouni, and S.E.Ealick (2005).
Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
  Acta Crystallogr D Biol Crystallogr, 61, 863-872.
PDB codes: 1u1c 1u1d 1u1e 1u1f 1u1g
14655027 J.Włodarczyk, G.Stoychev Galitonov, and B.Kierdaszuk (2004).
Identification of the tautomeric form of formycin A in its complex with Escherichia coli purine nucleoside phosphorylase based on the effect of enzyme-ligand binding on fluorescence and phosphorescence.
  Eur Biophys J, 33, 377-385.  
12937174 E.M.Bennett, C.Li, P.W.Allan, W.B.Parker, and S.E.Ealick (2003).
Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase.
  J Biol Chem, 278, 47110-47118.
PDB codes: 1pk7 1pk9 1pke 1pr0 1pr1 1pr2 1pr4 1pr5 1pr6 1pw7
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.