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PDBsum entry 1idt

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1idt
Jmol
Contents
Protein chains
217 a.a. *
Ligands
FMN ×2
CB1 ×2
Waters ×192
* Residue conservation analysis
PDB id:
1idt
Name: Oxidoreductase
Title: Structural studies on a prodrug-activating system-cb1954 and fmn-dependent nitroreductase
Structure: Minor fmn-dependent nitroreductase. Chain: a, b. Synonym: oxygen-insensitive NAD(p)h nitroreductase, dihydropteridine reductase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: nfnb or nfsi or nfsb or ntr or dpra or b0578. Expressed in: escherichia coli b. Expression_system_taxid: 37762.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.225     R-free:   0.269
Authors: E.Johansson,G.N.Parkinson,W.A.Denny,S.Neidle
Key ref: E.Johansson et al. (2003). Studies on the nitroreductase prodrug-activating system. Crystal structures of complexes with the inhibitor dicoumarol and dinitrobenzamide prodrugs and of the enzyme active form. J Med Chem, 46, 4009-4020. PubMed id: 12954054 DOI: 10.1021/jm030843b
Date:
05-Apr-01     Release date:   16-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38489  (NFNB_ECOLI) -  Oxygen-insensitive NAD(P)H nitroreductase
Seq:
Struc:
217 a.a.
217 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.5.1.34  - 6,7-dihydropteridine reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Biopterin Biosynthesis
      Reaction: A 5,6,7,8-tetrahydropteridine + NAD(P)(+) = a 6,7-dihydropteridine + NAD(P)H
5,6,7,8-tetrahydropteridine
+ NAD(P)(+)
= 6,7-dihydropteridine
+ NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     FAD binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/jm030843b J Med Chem 46:4009-4020 (2003)
PubMed id: 12954054  
 
 
Studies on the nitroreductase prodrug-activating system. Crystal structures of complexes with the inhibitor dicoumarol and dinitrobenzamide prodrugs and of the enzyme active form.
E.Johansson, G.N.Parkinson, W.A.Denny, S.Neidle.
 
  ABSTRACT  
 
The E. coli nitroreductase enzyme (NTR) has been widely used in suicide gene therapy (GDEPT and ADEPT) applications as a activating enzyme for nitroaromatic prodrugs of the dinitrobenzamide class. NTR has been previously shown to be a homodimeric enzyme with two active sites. We present here the crystal structures of the reduced form of NTR and its complexes with the inhibitor dicoumarol and three dinitrobenzamide prodrugs. Comparison of the structures of the oxidized and reduced forms of the native enzyme shows that the principal structural changes occur in the FMN cofactor and indicate that the enzyme itself is a relatively rigid structure that primarily provides a rigid structural framework on which hydride transfer occurs. The aziridinyldinitrobenzamide prodrug CB 1954 binds in nonidentical ways in both of the two active sites of the homodimeric enzyme, employing both hydrophobic and (in active site B) a direct H-bond contact to the side chain of Lys14. In active site A the 2-nitro group stacks above the FMN, and in active site B the 4-nitro group does, explaining why reduction of either nitro group is observed. In contrast, the larger mustard group of the dinitrobenzamide mustard compound SN 23862 forces the prodrug to bind at both active sites with only the 2-nitro group able to participate in hydride transfer from the FMN, explaining why only the 2-hydroxylamine reduction product is observed. In each site, the nitro groups of the prodrug make direct H-bond contacts with the enzyme; in active Site A the 2-nitro to Ser40 and the 4-nitro to Asn71, while in active Site B the 2-nitro contacts the main chain nitrogen of Thr41 and the 4-nitro group the Lys14 side chain. The related amide-substituted mustard SN 27217 binds in a broadly similar fashion, but with the larger amide group substituent able to reach and contact the side chain of Arg107, further restricting the prodrug conformations in the binding site. The inhibitor dicoumarol appears to bind primarily by pi-stacking interactions and hydrophobic contacts, with no conformational changes in the enzyme. One of the hydroxycoumarin subunits stacks above the plane of the FMN via pi-overlap with the isoalloxazine ring, penetrating deep into the groove, with the other less well-defined. These studies suggest guidelines for further prodrug design. Steric bulk (e.g., mustard rather than aziridine) on the ring can limit the possible binding orientations, and the reducible nitro group must be located para to the mustard. Substitution on the carboxamide side chain still allows the prodrugs to bind, but also limits their orientation in the binding site. Finally, modulating substrate specificity by alteration of the structure of the enzyme rather than the prodrug might usefully focus on modifying the Phe124 residue and those surrounding it.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20624223 G.Manina, M.Bellinzoni, M.R.Pasca, J.Neres, A.Milano, A.L.Ribeiro, S.Buroni, H.Skovierová, P.Dianišková, K.Mikušová, J.Marák, V.Makarov, D.Giganti, A.Haouz, A.P.Lucarelli, G.Degiacomi, A.Piazza, L.R.Chiarelli, E.De Rossi, E.Salina, S.T.Cole, P.M.Alzari, and G.Riccardi (2010).
Biological and structural characterization of the Mycobacterium smegmatis nitroreductase NfnB, and its role in benzothiazinone resistance.
  Mol Microbiol, 77, 1172-1185.
PDB codes: 2wzv 2wzw
20162181 Z.Rong, W.Du, Y.Wang, and L.Lu (2010).
Carbon supported Pt colloid as effective catalyst for selective hydrogenation of nitroarenes to arylhydroxylamines.
  Chem Commun (Camb), 46, 1559-1561.  
19286809 A.F.Tavares, L.S.Nobre, A.M.Melo, and L.M.Saraiva (2009).
A novel nitroreductase of Staphylococcus aureus with S-nitrosoglutathione reductase activity.
  J Bacteriol, 191, 3403-3406.  
19436071 S.R.Thomas, P.M.McTamney, J.M.Adler, N.Laronde-Leblanc, and S.E.Rokita (2009).
Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands.
  J Biol Chem, 284, 19659-19667.
PDB codes: 3gb5 3gfd 3gh8
18355273 M.D.Roldán, E.Pérez-Reinado, F.Castillo, and C.Moreno-Vivián (2008).
Reduction of polynitroaromatic compounds: the bacterial nitroreductases.
  FEMS Microbiol Rev, 32, 474-500.  
17975564 D.C.Singleton, D.Li, S.Y.Bai, S.P.Syddall, J.B.Smaill, Y.Shen, W.A.Denny, W.R.Wilson, and A.V.Patterson (2007).
The nitroreductase prodrug SN 28343 enhances the potency of systemically administered armed oncolytic adenovirus ONYX-411(NTR).
  Cancer Gene Ther, 14, 953-967.  
17277060 H.Iwaki, T.Muraki, S.Ishihara, Y.Hasegawa, K.N.Rankin, T.Sulea, J.Boyd, and P.C.Lau (2007).
Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis.
  J Bacteriol, 189, 3502-3514.  
17223324 H.Pisharath, J.M.Rhee, M.A.Swanson, S.D.Leach, and M.J.Parsons (2007).
Targeted ablation of beta cells in the embryonic zebrafish pancreas using E. coli nitroreductase.
  Mech Dev, 124, 218-229.  
17298443 K.Takeda, M.Iizuka, T.Watanabe, J.Nakagawa, S.Kawasaki, and Y.Niimura (2007).
Synechocystis DrgA protein functioning as nitroreductase and ferric reductase is capable of catalyzing the Fenton reaction.
  FEBS J, 274, 1318-1327.  
  17768344 M.M.AbuKhader, J.Heap, C.I.De Matteis, S.W.Doughty, N.Minton, and M.Paoli (2007).
Crystallization and preliminary X-ray characterization of the Bacillus amyloliquefaciens YwrO enzyme.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 746-750.  
17523848 W.R.Wilson, K.O.Hicks, S.M.Pullen, D.M.Ferry, N.A.Helsby, and A.V.Patterson (2007).
Bystander effects of bioreductive drugs: potential for exploiting pathological tumor hypoxia with dinitrobenzamide mustards.
  Radiat Res, 167, 625-636.  
17119634 Z.C.Symons, and N.C.Bruce (2006).
Bacterial pathways for degradation of nitroaromatics.
  Nat Prod Rep, 23, 845-850.  
15684426 P.R.Race, A.L.Lovering, R.M.Green, A.Ossor, S.A.White, P.F.Searle, C.J.Wrighton, and E.I.Hyde (2005).
Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme.
  J Biol Chem, 280, 13256-13264.
PDB codes: 1yki 1ylr 1ylu
16187099 R.Kutty, and G.N.Bennett (2005).
Biochemical characterization of trinitrotoluene transforming oxygen-insensitive nitroreductases from Clostridium acetobutylicum ATCC 824.
  Arch Microbiol, 184, 158-167.  
15566399 P.F.Searle, M.J.Chen, L.Hu, P.R.Race, A.L.Lovering, J.I.Grove, C.Guise, M.Jaberipour, N.D.James, V.Mautner, L.S.Young, D.J.Kerr, A.Mountain, S.A.White, and E.I.Hyde (2004).
Nitroreductase: a prodrug-activating enzyme for cancer gene therapy.
  Clin Exp Pharmacol Physiol, 31, 811-816.  
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.