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PDBsum entry 1b8n

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protein ligands metals links
Transferase PDB id
1b8n
Jmol
Contents
Protein chain
278 a.a. *
Ligands
PO4
IMG
Metals
_MG
Waters ×145
* Residue conservation analysis
PDB id:
1b8n
Name: Transferase
Title: Purine nucleoside phosphorylase
Structure: Purine nucleoside phosphorylase. Chain: a. Other_details: complexed with transition-state analogue 1,4 1,4-imino-1-(s)-(9-deazaguanin-9-yl)-d-ribitol
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: spleen
Biol. unit: Trimer (from PQS)
Resolution:
2.00Å     R-factor:   0.164     R-free:   0.246
Authors: A.A.Fedorov,G.A.Kicska,E.V.Fedorov,B.V.Strokopytov,P.C.Tyler R.H.Furneaux,V.L.Schramm,S.C.Almo
Key ref:
G.A.Kicska et al. (2002). Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase. Biochemistry, 41, 14489-14498. PubMed id: 12463747 DOI: 10.1021/bi026636f
Date:
02-Feb-99     Release date:   08-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P55859  (PNPH_BOVIN) -  Purine nucleoside phosphorylase
Seq:
Struc:
289 a.a.
278 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
Bound ligand (Het Group name = IMG)
matches with 58.33% similarity
+
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!
  Cellular component     cytoplasm   2 terms 
  Biological process     nucleobase-containing compound metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi026636f Biochemistry 41:14489-14498 (2002)
PubMed id: 12463747  
 
 
Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase.
G.A.Kicska, P.C.Tyler, G.B.Evans, R.H.Furneaux, W.Shi, A.Fedorov, A.Lewandowicz, S.M.Cahill, S.C.Almo, V.L.Schramm.
 
  ABSTRACT  
 
Immucillin-H (ImmH) and immucillin-G (ImmG) were previously reported as transition-state analogues for bovine purine nucleoside phosphorylase (PNP) and are the most powerful inhibitors reported for the enzyme (K(i) = 23 and 30 pM). Sixteen new immucillins are used to probe the atomic interactions that cause tight binding for bovine PNP. Eight analogues of ImmH are identified with equilibrium dissociation constants of 1 nM or below. A novel crystal structure of bovine PNP-ImmG-PO(4) is described. Crystal structures of ImmH and ImmG bound to bovine PNP indicate that nearly every H-bond donor/acceptor site on the inhibitor is fully engaged in favorable H-bond partners. Chemical modification of the immucillins is used to quantitate the energetics for each contact at the catalytic site. Conversion of the 6-carbonyl oxygen to a 6-amino group (ImmH to ImmA) increases the dissociation constant from 23 pM to 2.6 million pM. Conversion of the 4'-imino group to a 4'-oxygen (ImmH to 9-deazainosine) increases the dissociation constant from 23 pM to 2.0 million pM. Substituents that induce small pK(a) changes at N-7 demonstrate modest loss of affinity. Thus, 8-F or 8-CH(3)-substitutions decrease affinity less than 10-fold. But a change in the deazapurine ring to convert N-7 from a H-bond donor to a H-bond acceptor (ImmH to 4-aza-3-deaza-ImmH) decreases affinity by >10(7). Introduction of a methylene bridge between 9-deazahypoxanthine and the iminoribitol (9-(1'-CH(2))-ImmH) increased the distance between leaving and oxacarbenium groups and increased K(i) to 91 000 pM. Catalytic site energetics for 20 substitutions in the transition-state analogue are analyzed in this approach. Disruption of the H-bond pattern that defines the transition-state ensemble leads to a large decrease in binding affinity. Changes in a single H-bond contact site cause up to 10.1 kcal/mol loss of binding energy, requiring a cooperative H-bond pattern in binding the transition-state analogues. Groups involved in leaving group activation and ribooxacarbenium ion stabilization are central to the H-bond network that provides transition-state stabilization and tight binding of the immucillins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18001769 J.E.Lee, E.Bae, C.A.Bingman, G.N.Phillips, and R.T.Raines (2008).
Structural basis for catalysis by onconase.
  J Mol Biol, 375, 165-177.
PDB codes: 2gmk 2i5s
18234834 S.Saen-Oon, M.Ghanem, V.L.Schramm, and S.D.Schwartz (2008).
Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase.
  Biophys J, 94, 4078-4088.  
18801467 S.W.Ragsdale, and E.Pierce (2008).
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation.
  Biochim Biophys Acta, 1784, 1873-1898.  
18804699 S.W.Ragsdale (2008).
Catalysis of methyl group transfers involving tetrahydrofolate and B(12).
  Vitam Horm, 79, 293-324.  
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
17172470 T.I.Doukov, H.Hemmi, C.L.Drennan, and S.W.Ragsdale (2007).
Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases.
  J Biol Chem, 282, 6609-6618.
PDB codes: 2e7f 2ogy
17298059 V.Singh, and V.L.Schramm (2007).
Transition-state analysis of S. pneumoniae 5'-methylthioadenosine nucleosidase.
  J Am Chem Soc, 129, 2783-2795.  
15961383 A.Lewandowicz, E.A.Ringia, L.M.Ting, K.Kim, P.C.Tyler, G.B.Evans, O.V.Zubkova, S.Mee, G.F.Painter, D.H.Lenz, R.H.Furneaux, and V.L.Schramm (2005).
Energetic mapping of transition state analogue interactions with human and Plasmodium falciparum purine nucleoside phosphorylases.
  J Biol Chem, 280, 30320-30328.  
15746096 J.E.Lee, V.Singh, G.B.Evans, P.C.Tyler, R.H.Furneaux, K.A.Cornell, M.K.Riscoe, V.L.Schramm, and P.L.Howell (2005).
Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
  J Biol Chem, 280, 18274-18282.
PDB codes: 1y6q 1y6r
14752199 J.C.Evans, D.P.Huddler, M.T.Hilgers, G.Romanchuk, R.G.Matthews, and M.L.Ludwig (2004).
Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.
  Proc Natl Acad Sci U S A, 101, 3729-3736.
PDB codes: 1q7m 1q7q 1q7z 1q85 1q8a 1q8j
12842889 A.Lewandowicz, P.C.Tyler, G.B.Evans, R.H.Furneaux, and V.L.Schramm (2003).
Achieving the ultimate physiological goal in transition state analogue inhibitors for purine nucleoside phosphorylase.
  J Biol Chem, 278, 31465-31468.  
12704087 D.A.Kraut, K.S.Carroll, and D.Herschlag (2003).
Challenges in enzyme mechanism and energetics.
  Annu Rev Biochem, 72, 517-571.  
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.