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PDBsum entry 2oc9

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protein ligands links
Transferase PDB id
2oc9
Jmol
Contents
Protein chain
278 a.a. *
Ligands
PO4
IMH
Waters ×56
* Residue conservation analysis
PDB id:
2oc9
Name: Transferase
Title: Crystal stucture of human purine nucleoside phosphorylase mu with imm-h
Structure: Purine nucleoside phosphorylase. Chain: a. Fragment: purine nucleoside phosphorylase. Synonym: inosine phosphorylase. Pnp. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: np, pnp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.59Å     R-factor:   0.197     R-free:   0.243
Authors: A.Rinaldo-Matthis,S.C.Almo,V.L.Schramm
Key ref: A.S.Murkin et al. (2007). Neighboring group participation in the transition state of human purine nucleoside phosphorylase. Biochemistry, 46, 5038-5049. PubMed id: 17407325
Date:
20-Dec-06     Release date:   22-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase
Seq:
Struc:
289 a.a.
278 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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 = IMH)
matches with 60.87% 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     intracellular   5 terms 
  Biological process     small molecule metabolic process   16 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
Biochemistry 46:5038-5049 (2007)
PubMed id: 17407325  
 
 
Neighboring group participation in the transition state of human purine nucleoside phosphorylase.
A.S.Murkin, M.R.Birck, A.Rinaldo-Matthis, W.Shi, E.A.Taylor, S.C.Almo, V.L.Schramm.
 
  ABSTRACT  
 
The X-ray crystal structures of human purine nucleoside phosphorylase (PNP) with bound inosine or transition-state analogues show His257 within hydrogen bonding distance of the 5'-hydroxyl. The mutants His257Phe, His257Gly, and His257Asp exhibited greatly decreased affinity for Immucillin-H (ImmH), binding this mimic of an early transition state as much as 370-fold (Km/Ki) less tightly than native PNP. In contrast, these mutants bound DADMe-ImmH, a mimic of a late transition state, nearly as well as the native enzyme. These results indicate that His257 serves an important role in the early stages of transition-state formation. Whereas mutation of His257 resulted in little variation in the PNP x DADMe-ImmH x SO4 structures, His257Phe x ImmH x PO4 showed distortion at the 5'-hydroxyl, indicating the importance of H-bonding in positioning this group during progression to the transition state. Binding isotope effect (BIE) and kinetic isotope effect (KIE) studies of the remote 5'-(3)H for the arsenolysis of inosine with native PNP revealed a BIE of 1.5% and an unexpectedly large intrinsic KIE of 4.6%. This result is interpreted as a moderate electronic distortion toward the transition state in the Michaelis complex with continued development of a similar distortion at the transition state. The mutants His257Phe, His257Gly, and His257Asp altered the 5'-(3)H intrinsic KIE to -3, -14, and 7%, respectively, while the BIEs contributed 2, 2, and -2%, respectively. These surprising results establish that forces in the Michaelis complex, reported by the BIEs, can be reversed or enhanced at the transition state.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20203397 G.J.Gainsford, R.H.Furneaux, P.C.Tyler, A.Sauve, and V.L.Shramm (2010).
A synchrotron radiation study of the one-dimensional complex of sodium with (1S)-N-carboxylato-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol, a member of the 'immucillin' family.
  Acta Crystallogr C, 66, m65-m68.  
20212140 M.C.Ho, W.Shi, A.Rinaldo-Matthis, P.C.Tyler, G.B.Evans, K.Clinch, S.C.Almo, and V.L.Schramm (2010).
Four generations of transition-state analogues for human purine nucleoside phosphorylase.
  Proc Natl Acad Sci U S A, 107, 4805-4812.  
19170524 K.Clinch, G.B.Evans, R.F.Fröhlich, R.H.Furneaux, P.M.Kelly, L.Legentil, A.S.Murkin, L.Li, V.L.Schramm, P.C.Tyler, and A.D.Woolhouse (2009).
Third-generation immucillins: syntheses and bioactivities of acyclic immucillin inhibitors of human purine nucleoside phosphorylase.
  J Med Chem, 52, 1126-1143.  
19156310 M.E.Soliman, G.D.Ruggiero, J.J.Pernía, I.R.Greig, and I.H.Williams (2009).
Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases.
  Org Biomol Chem, 7, 460-468.  
19778725 M.Ghanem, A.S.Murkin, and V.L.Schramm (2009).
Ribocation transition state capture and rebound in human purine nucleoside phosphorylase.
  Chem Biol, 16, 971-979.  
19569683 N.R.McIntyre, E.W.Lowe, and D.J.Merkler (2009).
Imino-oxy acetic acid dealkylation as evidence for an inner-sphere alcohol intermediate in the reaction catalyzed by peptidylglycine alpha-hydroxylating monooxygenase.
  J Am Chem Soc, 131, 10308-10319.  
19620996 S.D.Schwartz, and V.L.Schramm (2009).
Enzymatic transition states and dynamic motion in barrier crossing.
  Nat Chem Biol, 5, 551-558.  
18154341 A.Rinaldo-Matthis, A.S.Murkin, U.A.Ramagopal, K.Clinch, S.P.Mee, G.B.Evans, P.C.Tyler, R.H.Furneaux, S.C.Almo, and V.L.Schramm (2008).
L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.
  J Am Chem Soc, 130, 842-844.
PDB codes: 2q7o 3bgs
18778937 A.S.Murkin, K.Clinch, J.M.Mason, P.C.Tyler, and V.L.Schramm (2008).
Immucillins in custom catalytic-site cavities.
  Bioorg Med Chem Lett, 18, 5900-5903.  
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.  
18946041 S.Saen-Oon, S.Quaytman-Machleder, V.L.Schramm, and S.D.Schwartz (2008).
Atomic detail of chemical transformation at the transition state of an enzymatic reaction.
  Proc Natl Acad Sci U S A, 105, 16543-16548.  
  20664707 S.Saen-Oon, V.L.Schramm, and S.D.Schwartz (2008).
Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase.
  Z Phys Chem (N F), 222, 1359-1374.  
17803683 A.Schwarz, L.Brecker, and B.Nidetzky (2007).
Probing the active site of Corynebacterium callunae starch phosphorylase through the characterization of wild-type and His334-->Gly mutant enzymes.
  FEBS J, 274, 5105-5115.  
17869163 V.L.Schramm (2007).
Binding isotope effects: boon and bane.
  Curr Opin Chem Biol, 11, 529-536.  
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.