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PDBsum entry 1qe5

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1qe5
Jmol
Contents
Protein chains
266 a.a. *
Ligands
PO4 ×3
Metals
_CA
Waters ×262
* Residue conservation analysis
PDB id:
1qe5
Name: Transferase
Title: Purine nucleoside phosphorylase from cellulomonas sp. In complex with phosphate
Structure: Pentosyltransferase. Chain: a, b, c. Fragment: residues 9-282. Ec: 2.4.2.1
Source: Cellulomonas sp.. Organism_taxid: 40001
Biol. unit: Trimer (from PQS)
Resolution:
2.20Å     R-factor:   0.200     R-free:   0.260
Authors: J.Tebbe,A.Bzowska,B.Wielgus-Kutrowska,W.Schroeder, Z.Kazimierczuk,D.Shugar,W.Saenger,G.Koellner
Key ref:
J.Tebbe et al. (1999). Crystal structure of the purine nucleoside phosphorylase (PNP) from Cellulomonas sp. and its implication for the mechanism of trimeric PNPs. J Mol Biol, 294, 1239-1255. PubMed id: 10600382 DOI: 10.1006/jmbi.1999.3327
Date:
13-Jul-99     Release date:   12-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P81989  (PUNA_CELSP) -  Purine nucleoside phosphorylase
Seq:
Struc:
282 a.a.
266 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.1  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
+
phosphate
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!
  Biological process     nucleobase-containing compound metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.3327 J Mol Biol 294:1239-1255 (1999)
PubMed id: 10600382  
 
 
Crystal structure of the purine nucleoside phosphorylase (PNP) from Cellulomonas sp. and its implication for the mechanism of trimeric PNPs.
J.Tebbe, A.Bzowska, B.Wielgus-Kutrowska, W.Schröder, Z.Kazimierczuk, D.Shugar, W.Saenger, G.Koellner.
 
  ABSTRACT  
 
The three-dimensional structure of the trimeric purine nucleoside phosphorylase (PNP) from Cellulomonas sp. has been determined by X-ray crystallography. The binary complex of the enzyme with orthophosphate was crystallized in the orthorhombic space group P212121 with unit cell dimensions a=64.1 A, b=108.9 A, c=119.3 A and an enzymatically active trimer in the asymmetric unit. X-ray data were collected at 4 degrees C using synchrotron radiation (EMBL/DESY, Hamburg). The structure was solved by molecular replacement, with the calf spleen PNP structure as a model, and refined at 2.2 A resolution. The ternary "dead-end" complex of the enzyme with orthophosphate and 8-iodoguanine was obtained by soaking crystals of the binary orthophosphate complex with the very weak substrate 8-iodoguanosine. Data were collected at 100 K with CuKalpha radiation, and the three-dimensional structure refined at 2.4 A resolution. Although the sequence of the Cellulomonas PNP shares only 33 % identity with the calf spleen enzyme, and almost no identity with the hexameric Escherichia coli PNP, all three enzymes have many common structural features, viz. the nine-stranded central beta-sheet, the positions of the active centres, and the geometrical arrangement of the ligands in the active centres. Some similarities of the surrounding helices also prevail. In Cellulomonas PNP, each of the three active centres per trimer is occupied by orthophosphate, and by orthophosphate and base, respectively, and small structural differences between monomers A, B and C are observed. This supports cooperativity between subunits (non-identity of binding sites) rather than existence of more than one binding site per monomer, as previously suggested for binding of phosphate by mammalian PNPs. The phosphate binding site is located between two conserved beta- and gamma-turns and consists of Ser46, Arg103, His105, Gly135 and Ser223, and one or two water molecules. The guanine base is recognized by a zig-zag pattern of possible hydrogen bonds, as follows: guanine N-1...Glu204 O(epsilon1)...guanine NH2...Glu204 O(epsilon2). The exocyclic O6 of the base is bridged via a water molecule to Asn246 N(delta), which accounts for the inhibitory, but lack of substrate, activity of adenosine. An alternative molecular mechanism for catalysis by trimeric PNPs is proposed, in which the key catalytic role is played by Glu204 (Glu201 in the calf and human enzymes), while Asn246 (Asn243 in the mammalian enzymes) supports binding of 6-oxopurines rather than catalysis. This mechanism, in contrast to that previously suggested, is consistent with the excellent substrate properties of N-7 substituted nucleosides, the specificity of trimeric PNPs versus 6-oxopurine nucleosides and the reported kinetic properties of Glu201/Ala and Asn243/Ala point variants of human PNP.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Complex of the trimeric Cellulomonas PNP with phosphate, showing one phosphate per monomer, indicated in red (oxygen atoms). The trimer is viewed along the 3-fold non-crystallographic axis. In each monomer the long loop (in magenta) between strand b6 and helix aV, belting the monomer from one side, and the peripheral helix aVI (compared with Figure 1(a)), are responsible for trimer formation. The location of the calcium ion at the periphery of monomer B, forming crystal packing contacts, is indicated in orange. For com- parison with Figure 1(a), several structural elements in monomer A are labelled (all helices and two strands). Drawn with MOLSCRIPT (Kraulis, 1991).
Figure 5.
Figure 5. (a) Structures of unusual substrates of mam- malian PNPs: 3-b-Ado, NiR and m 7 Guo. For m 7 Guo the two possible ionic forms, cation and zwitterion, are shown (Shugar & Psoda, 1990). The cationic form is the
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 294, 1239-1255) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20799866 A.Al-Kali, V.Gandhi, M.Ayoubi, M.Keating, and F.Ravandi (2010).
Forodesine: review of preclinical and clinical data.
  Future Oncol, 6, 1211-1217.  
20057051 H.M.Pereira, M.M.Rezende, M.S.Castilho, G.Oliva, and R.C.Garratt (2010).
Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni.
  Acta Crystallogr D Biol Crystallogr, 66, 73-79.
PDB codes: 3e9r 3f8w 3faz 3fnq
20124695 Y.N.Kang, Y.Zhang, P.W.Allan, W.B.Parker, J.W.Ting, C.Y.Chang, and S.E.Ealick (2010).
Structure of grouper iridovirus purine nucleoside phosphorylase.
  Acta Crystallogr D Biol Crystallogr, 66, 155-162.
PDB code: 3khs
19474219 B.Németi, and Z.Gregus (2009).
Mechanism of thiol-supported arsenate reduction mediated by phosphorolytic-arsenolytic enzymes: I. The role of arsenolysis.
  Toxicol Sci, 110, 270-281.  
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.  
17107284 F.Ravandi, and V.Gandhi (2006).
Novel purine nucleoside analogues for T-cell-lineage acute lymphoblastic leukaemia and lymphoma.
  Expert Opin Investig Drugs, 15, 1601-1613.  
  16511035 M.V.Dontsova, A.G.Gabdoulkhakov, O.K.Molchan, A.A.Lashkov, M.B.Garber, A.S.Mironov, N.E.Zhukhlistova, E.Y.Morgunova, W.Voelter, C.Betzel, Y.Zhang, S.E.Ealick, and A.M.Mikhailov (2005).
Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline state.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 337-340.
PDB code: 1sj9
16131572 V.Gandhi, J.M.Kilpatrick, W.Plunkett, M.Ayres, L.Harman, M.Du, S.Bantia, J.Davisson, W.G.Wierda, S.Faderl, H.Kantarjian, and D.Thomas (2005).
A proof-of-principle pharmacokinetic, pharmacodynamic, and clinical study with purine nucleoside phosphorylase inhibitor immucillin-H (BCX-1777, forodesine).
  Blood, 106, 4253-4260.  
15272165 M.Luić, G.Koellner, T.Yokomatsu, S.Shibuya, and A.Bzowska (2004).
Calf spleen purine-nucleoside phosphorylase: crystal structure of the binary complex with a potent multisubstrate analogue inhibitor.
  Acta Crystallogr D Biol Crystallogr, 60, 1417-1424.
PDB code: 1v48
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
12180982 G.Stoychev, B.Kierdaszuk, and D.Shugar (2002).
Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems.
  Eur J Biochem, 269, 4048-4057.  
11489901 T.C.Appleby, I.I.Mathews, M.Porcelli, G.Cacciapuoti, and S.E.Ealick (2001).
Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
  J Biol Chem, 276, 39232-39242.
PDB codes: 1jds 1jdt 1jdu 1jdv 1jdz 1je0 1je1 1jp7 1jpv
11337031 A.Bzowska, E.Kulikowska, and D.Shugar (2000).
Purine nucleoside phosphorylases: properties, functions, and clinical aspects.
  Pharmacol Ther, 88, 349-425.  
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.