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PDBsum entry 1sm8

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1sm8
Jmol
Contents
Protein chains
131 a.a. *
Ligands
NO3
DUT ×3
TRS
Metals
_CR ×3
Waters ×8
* Residue conservation analysis
PDB id:
1sm8
Name: Hydrolase
Title: M. Tuberculosis dutpase complexed with chromium and dutp
Structure: Deoxyuridine 5'-triphosphate nucleotidohydrolase. Chain: a, b, c. Synonym: dutpase, dutp pyrophosphatase. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: dut, rv2697c, mt2771, mtcy05a6.18c, mb2716c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.90Å     R-factor:   0.235     R-free:   0.282
Authors: M.R.Sawaya,S.Chan,B.Segelke,T.Lekin,H.Krupka,U.S.Cho,M.- Y.Kim,M.So,C.-Y.Kim,C.M.Naranjo,Y.C.Rogers,M.S.Park, G.S.Waldo,I.Pashkov,D.Cascio,T.O.Yeates,J.L.Perry, T.C.Terwilliger,D.Eisenberg,Tb Structural Genomics Consortium (Tbsgc)
Key ref:
S.Chan et al. (2004). Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism. J Mol Biol, 341, 503-517. PubMed id: 15276840 DOI: 10.1016/j.jmb.2004.06.028
Date:
08-Mar-04     Release date:   16-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WNS5  (DUT_MYCTU) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase
Seq:
Struc:
154 a.a.
131 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.23  - dUTP diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dUTP + H2O = dUMP + diphosphate
dUTP
Bound ligand (Het Group name = DUT)
corresponds exactly
+ H(2)O
= dUMP
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     growth   5 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.06.028 J Mol Biol 341:503-517 (2004)
PubMed id: 15276840  
 
 
Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.
S.Chan, B.Segelke, T.Lekin, H.Krupka, U.S.Cho, M.Y.Kim, M.So, C.Y.Kim, C.M.Naranjo, Y.C.Rogers, M.S.Park, G.S.Waldo, I.Pashkov, D.Cascio, J.L.Perry, M.R.Sawaya.
 
  ABSTRACT  
 
The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. dUTPase·Mg2+·a,b-imido dUTP complex (PDB ID 1six). (a) Stereo view of the active site. The a,b-imido dUTP atoms are colored by atom type. Enzyme residues are colored according to conserved motif. Colors are as follows: motif I (blue), motif II (green), motif III (yellow), motif IV (orange), motif V (red). The active site is a composite of all three molecules. Motifs I, II, and IV are contributed by molecule A. Motif III is contributed by molecule B. Motif V is contributed by molecule C. (b) Simulated annealing omit map showing the density for the ligand, magnesium, and coordinated water molecules (1.6 Å resolution, contoured at 4.2s). Density is also shown for the proposed nucleophilic water molecule, 336. (c) Schematic of the dUTPase reaction mechanism.
Figure 4.
Figure 4. Comparison of conformation of Mg2+·a,b-imido dUTP bound to dUTPase with the conformation of the incoming ddCTP in DNA polymerase b (1bpy). (The 3'-hydroxyl of the primer was modeled based on the position of the dideoxyribose ring.) Both enzymes use a metal ion to coordinate the triphosphate moiety with a,b,g tridentate geometry. Both enzymes catalyze the in-line nucleophilic attack on the a-phosphorus of a dNTP. Even the nucleophiles in both enzymes have the same position with respect to the a-phosphorus. The difference is that the nucleophile in the polymerase reaction is the 3'-hydroxyl of the primer strand rather than a water molecule as it is in dUTPase.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 503-517) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460457 S.McNicholas, E.Potterton, K.S.Wilson, and M.E.Noble (2011).
Presenting your structures: the CCP4mgmolecular-graphics software.
  Acta Crystallogr D Biol Crystallogr, 67, 386-394.  
  20865174 C.Mura, C.M.McCrimmon, J.Vertrees, and M.R.Sawaya (2010).
An introduction to biomolecular graphics.
  PLoS Comput Biol, 6, 0.  
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
20823546 J.García-Nafría, L.Burchell, M.Takezawa, N.J.Rzechorzek, M.J.Fogg, and K.S.Wilson (2010).
The structure of the genomic Bacillus subtilis dUTPase: novel features in the Phe-lid.
  Acta Crystallogr D Biol Crystallogr, 66, 953-961.
PDB codes: 2xcd 2xce
20473284 M.A.Tormo-Más, I.Mir, A.Shrestha, S.M.Tallent, S.Campoy, I.Lasa, J.Barbé, R.P.Novick, G.E.Christie, and J.R.Penadés (2010).
Moonlighting bacteriophage proteins derepress staphylococcal pathogenicity islands.
  Nature, 465, 779-782.  
20634809 R.P.Novick, G.E.Christie, and J.R.Penadés (2010).
The phage-related chromosomal islands of Gram-positive bacteria.
  Nat Rev Microbiol, 8, 541-551.  
18837522 B.G.Vértessy, and J.Tóth (2009).
Keeping uracil out of DNA: physiological role, structure and catalytic mechanism of dUTPases.
  Acc Chem Res, 42, 97.  
19586911 L.Freeman, M.Buisson, N.Tarbouriech, A.Van der Heyden, P.Labbé, and W.P.Burmeister (2009).
The flexible motif V of Epstein-Barr virus deoxyuridine 5'-triphosphate pyrophosphatase is essential for catalysis.
  J Biol Chem, 284, 25280-25289.
PDB codes: 2we0 2we1 2we2 2we3
17932923 J.Kovári, O.Barabás, B.Varga, A.Békési, F.Tölgyesi, J.Fidy, J.Nagy, and B.G.Vértessy (2008).
Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
  Proteins, 71, 308-319.
PDB codes: 2hr6 2hrm
18471977 V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, and S.H.Wilson (2008).
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
  Mol Cell, 30, 315-324.
PDB codes: 3c2k 3c2l 3c2m
17452782 A.Samal, N.Schormann, W.J.Cook, L.J.DeLucas, and D.Chattopadhyay (2007).
Structures of vaccinia virus dUTPase and its nucleotide complexes.
  Acta Crystallogr D Biol Crystallogr, 63, 571-580.
PDB codes: 2okb 2okd 2oke 2ol0 2ol1
17651436 E.Johansson, M.Thymark, J.H.Bynck, M.Fanø, S.Larsen, and M.Willemoës (2007).
Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme.
  FEBS J, 274, 4188-4198.
PDB codes: 2j4h 2j4q
  17565183 M.Bajaj, and H.Moriyama (2007).
Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 409-411.
PDB code: 2pc5
16441668 A.Guranowski, E.StarzyƄska, M.Pietrowska-Borek, J.Jemielity, J.Kowalska, E.Darzynkiewicz, M.J.Thompson, and G.M.Blackburn (2006).
Methylene analogues of adenosine 5'-tetraphosphate. Their chemical synthesis and recognition by human and plant mononucleoside tetraphosphatases and dinucleoside tetraphosphatases.
  FEBS J, 273, 829-838.  
16359314 M.Y.Galperin, O.V.Moroz, K.S.Wilson, and A.G.Murzin (2006).
House cleaning, a part of good housekeeping.
  Mol Microbiol, 59, 5.  
15539408 E.Johansson, M.Fanø, J.H.Bynck, J.Neuhard, S.Larsen, B.W.Sigurskjold, U.Christensen, and M.Willemoës (2005).
Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes.
  J Biol Chem, 280, 3051-3059.
PDB codes: 1xs1 1xs4 1xs6
16154087 N.Tarbouriech, M.Buisson, J.M.Seigneurin, S.Cusack, and W.P.Burmeister (2005).
The monomeric dUTPase from Epstein-Barr virus mimics trimeric dUTPases.
  Structure, 13, 1299-1310.
PDB codes: 2bsy 2bt1
15735341 P.Müller, M.R.Sawaya, I.Pashkov, S.Chan, C.Nguyen, Y.Wu, L.J.Perry, and D.Eisenberg (2005).
The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.
  Acta Crystallogr D Biol Crystallogr, 61, 309-315.
PDB code: 1rii
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.