PDBsum entry 1r4f

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
314 a.a. *
_CA ×2
Waters ×163
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Inosine-adenosine-guanosine preferring nucleoside hydrolase from trypanosoma vivax: trp260ala mutant in complex with 3- deaza-adenosine
Structure: Iag-nucleoside hydrolase. Chain: a, b. Fragment: iag-nh. Engineered: yes. Mutation: yes
Source: Trypanosoma vivax. Organism_taxid: 5699. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.205     R-free:   0.257
Authors: W.Versees,S.Loverix,A.Vandemeulebroucke,P.Geerlings, J.Steyaert
Key ref:
W.Versées et al. (2004). Leaving group activation by aromatic stacking: an alternative to general acid catalysis. J Mol Biol, 338, 1-6. PubMed id: 15050818 DOI: 10.1016/j.jmb.2004.02.049
06-Oct-03     Release date:   13-Apr-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9GPQ4  (Q9GPQ4_TRYVI) -  IAG-nucleoside hydrolase
327 a.a.
314 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  


DOI no: 10.1016/j.jmb.2004.02.049 J Mol Biol 338:1-6 (2004)
PubMed id: 15050818  
Leaving group activation by aromatic stacking: an alternative to general acid catalysis.
W.Versées, S.Loverix, A.Vandemeulebroucke, P.Geerlings, J.Steyaert.
General acid catalysis is a powerful and widely used strategy in enzymatic nucleophilic displacement reactions. For example, hydrolysis/phosphorolysis of the N-glycosidic bond in nucleosides and nucleotides commonly involves the protonation of the leaving nucleobase concomitant with nucleophilic attack. However, in the nucleoside hydrolase of the parasite Trypanosoma vivax, crystallographic and mutagenesis studies failed to identify a general acid. This enzyme binds the purine base of the substrate between the aromatic side-chains of Trp83 and Trp260. Here, we show via quantum chemical calculations that face-to-face stacking can raise the pKa of a heterocyclic aromatic compound by several units. Site-directed mutagenesis combined with substrate engineering demonstrates that Trp260 catalyzes the cleavage of the glycosidic bond by promoting the protonation of the purine base at N-7, hence functioning as an alternative to general acid catalysis.
  Selected figure(s)  
Figure 1.
Figure 1. Active site of the slow Asp10Ala mutant of the T. vivax nucleoside hydrolase in complex with the substrate inosine (PDB entry 1KIC). The carbon atoms of inosine are shown in dark gray. Trp260, which stacks to the purine base, is shown in green. The other active site residues are colored light gray. A Ca^2+ at the bottom of the active site is depicted as a dark blue sphere. The nucleophilic water and the water molecule hydrogen bonded to the N-7 of inosine are depicted as light blue spheres.
Figure 2.
Figure 2. Stereo view showing the superposition of the active sites of wild-type T. vivax nucleoside hydrolase (grey, PDB entry 1HP0, subunit B) and of the Trp260Ala mutant (yellow, PDB entry 1R4F, subunit B), both complexed with the competitive inhibitor 3-deaza-adenosine (drawn in thicker lines). The Ca^2+ at the bottom of the active site and the nucleophilic water molecule are depicted as a large and a small sphere, respectively. The side-chains of all relevant active site residues as well as the loop segment connecting Glu82 to Arg84 are shown.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 338, 1-6) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21267490 A.Ebrahimi, M.Habibi-Khorassani, and S.Bazzi (2011).
The impact of protonation and deprotonation of 3-methyl-2'-deoxyadenosine on N-glycosidic bond cleavage.
  Phys Chem Chem Phys, 13, 3334-3343.  
20601405 I.Pecsi, I.Leveles, V.Harmat, B.G.Vertessy, and J.Toth (2010).
Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase.
  Nucleic Acids Res, 38, 7179-7186.
PDB codes: 3hza 3loj
19425763 A.Krishtal, K.Vanommeslaeghe, A.Olasz, T.Veszprémi, C.Van Alsenoy, and P.Geerlings (2009).
Accurate interaction energies at density functional theory level by means of an efficient dispersion correction.
  J Chem Phys, 130, 174101.  
19920175 M.C.Ho, M.B.Sturm, S.C.Almo, and V.L.Schramm (2009).
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
  Proc Natl Acad Sci U S A, 106, 20276-20281.
PDB codes: 3hio 3hiq 3his 3hit 3hiv 3hiw
18519562 A.Vandemeulebroucke, S.De Vos, E.Van Holsbeke, J.Steyaert, and W.Versées (2008).
A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from trypanosoma vivax.
  J Biol Chem, 283, 22272-22282.
PDB code: 3b9g
18940667 Q.Liu, I.A.Kriksunov, H.Jiang, R.Graeff, H.Lin, H.C.Lee, and Q.Hao (2008).
Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38.
  Chem Biol, 15, 1068-1078.
PDB codes: 3dzf 3dzg 3dzh 3dzi 3dzj 3dzk
18081388 A.Olasz, K.Vanommeslaeghe, A.Krishtal, T.Veszprémi, C.Van Alsenoy, and P.Geerlings (2007).
The use of atomic intrinsic polarizabilities in the evaluation of the dispersion energy.
  J Chem Phys, 127, 224105.  
16607668 G.Roos, S.Loverix, E.Brosens, K.Van Belle, L.Wyns, P.Geerlings, and J.Messens (2006).
The activation of electrophile, nucleophile and leaving group during the reaction catalysed by pI258 arsenate reductase.
  Chembiochem, 7, 981-989.  
15878665 K.Vanommeslaeghe, F.De Proft, S.Loverix, D.Tourwé, and P.Geerlings (2005).
Theoretical study revealing the functioning of a novel combination of catalytic motifs in histone deacetylase.
  Bioorg Med Chem, 13, 3987-3992.  
15788750 P.Mignon, S.Loverix, J.Steyaert, and P.Geerlings (2005).
Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases.
  Nucleic Acids Res, 33, 1779-1789.  
15695817 S.Loverix, P.Geerlings, M.McNaughton, K.Augustyns, A.Vandemeulebroucke, J.Steyaert, and W.Versées (2005).
Substrate-assisted leaving group activation in enzyme-catalyzed N-glycosidic bond cleavage.
  J Biol Chem, 280, 14799-14802.  
15556411 F.A.Anet (2004).
The place of metabolism in the origin of life.
  Curr Opin Chem Biol, 8, 654-659.  
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.