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PDBsum entry 1ylu

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ylu
Jmol
Contents
Protein chains
216 a.a. *
Ligands
ACT ×3
FMN ×2
Waters ×528
* Residue conservation analysis
PDB id:
1ylu
Name: Oxidoreductase
Title: The structure of e. Coli nitroreductase with bound acetate, crystal form 2
Structure: Oxygen-insensitive NAD(p)h nitroreductase. Chain: a, b. Synonym: fmn-dependent nitroreductase, dihydropteridine reductase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: nfnb, dpra, nfsb, nfsi, ntr. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.147     R-free:   0.203
Authors: P.R.Race,A.L.Lovering,R.M.Green,A.Ossor,S.A.White, P.F.Searle,C.J.Wrighton,E.I.Hyde
Key ref:
P.R.Race et al. (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. PubMed id: 15684426 DOI: 10.1074/jbc.M409652200
Date:
19-Jan-05     Release date:   08-Feb-05    
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.
216 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: 10.1074/jbc.M409652200 J Biol Chem 280:13256-13264 (2005)
PubMed id: 15684426  
 
 
Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme.
P.R.Race, A.L.Lovering, R.M.Green, A.Ossor, S.A.White, P.F.Searle, C.J.Wrighton, E.I.Hyde.
 
  ABSTRACT  
 
The antibiotics nitrofurazone and nitrofurantoin are used in the treatment of genitourinary infections and as topical antibacterial agents. Their action is dependent upon activation by bacterial nitroreductase flavoproteins, including the Escherichia coli nitroreductase (NTR). Here we show that the products of reduction of these antibiotics by NTR are the hydroxylamine derivatives. We show that the reduction of nitrosoaromatics is enzyme-catalyzed, with a specificity constant approximately 10,000-fold greater than that of the starting nitro compounds. This suggests that the reduction of nitro groups proceeds through two successive, enzyme-mediated reactions and explains why the nitroso intermediates are not observed. The global reaction rate for nitrofurazone determined in this study is over 10-fold higher than that previously reported, suggesting that the enzyme is much more active toward nitroaromatics than previously estimated. Surprisingly, in the crystal structure of the oxidized NTR-nitrofurazone complex, nitrofurazone is oriented with its amide group, rather than the nitro group to be reduced, positioned over the reactive N5 of the FMN cofactor. Free acetate, which acts as a competitive inhibitor with respect to NADH, binds in a similar orientation. We infer that the orientation of bound nitrofurazone depends upon the redox state of the enzyme. We propose that the charge distribution on the FMN rings, which alters upon reduction, is an important determinant of substrate binding and reactivity in flavoproteins with broad substrate specificity.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Chemical structures of nitrofurazone (A) and nitrofurantoin (B). In A, the numbering of the atoms used throughout is shown.
Figure 2.
FIG. 2. Refined electron density maps of NFZ (A) and acetate (ACT)(B) in the active site of NTR; 2mF[o] - DF[c], SIGMAA-weighted, contoured at 1 , resolution of 1.7 Å. C, schematic stereoview of contacts formed in A. Residues in the active site are shaded by atom type and labeled. S40', T41' and F124' come from a different subunit in the dimer from F70, N71, and E165. Water molecules forming hydrogen bonds to the ligands are shown as circles. Hydrogen bonds are shown as dashed lines.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 13256-13264) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20857287 Y.Qu, H.Zhou, A.Li, F.Ma, and J.Zhou (2011).
Nitroreductase activity of ferredoxin reductase BphA4 from Dyella ginsengisoli LA-4 by catalytic and structural properties analysis.
  Appl Microbiol Biotechnol, 89, 655-663.  
20439607 A.Y.Sokolova, S.Wyllie, S.Patterson, S.L.Oza, K.D.Read, and A.H.Fairlamb (2010).
Cross-resistance to nitro drugs and implications for treatment of human African trypanosomiasis.
  Antimicrob Agents Chemother, 54, 2893-2900.  
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
20508930 Y.Yin, Y.Xiao, H.Z.Liu, F.Hao, S.Rayner, H.Tang, and N.Y.Zhou (2010).
Characterization of catabolic meta-nitrophenol nitroreductase from Cupriavidus necator JMP134.
  Appl Microbiol Biotechnol, 87, 2077-2085.  
19930647 D.C.Stein, E.Carrizosa, and S.Dunham (2009).
Use of nfsB, encoding nitroreductase, as a reporter gene to determine the mutational spectrum of spontaneous mutations in Neisseria gonorrhoeae.
  BMC Microbiol, 9, 239.  
19438716 I.N.Olekhnovich, A.Goodwin, and P.S.Hoffman (2009).
Characterization of the NAD(P)H oxidase and metronidazole reductase activities of the RdxA nitroreductase of Helicobacter pylori.
  FEBS J, 276, 3354-3364.  
19455141 S.O.Vass, D.Jarrom, W.R.Wilson, E.I.Hyde, and P.F.Searle (2009).
E. coli NfsA: an alternative nitroreductase for prodrug activation gene therapy in combination with CB1954.
  Br J Cancer, 100, 1903-1911.  
18720338 D.J.Brondani, N.Caetano, D.R.Moreira, R.R.Soares, V.T.Lima, J.M.de Araújo, F.C.de Abreu, B.G.de Oliveira, M.Z.Hernandes, and A.C.Leite (2008).
Novel nitrofurazone derivatives endowed with antimicrobial activity.
  Arch Pharm (Weinheim), 341, 655-660.  
18355323 E.Pérez-Reinado, M.D.Roldán, F.Castillo, and C.Moreno-Vivián (2008).
The NprA nitroreductase required for 2,4-dinitrophenol reduction in Rhodobacter capsulatus is a dihydropteridine reductase.
  Environ Microbiol, 10, 3174-3183.  
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.  
17301844 C.P.Guise, J.I.Grove, E.I.Hyde, and P.F.Searle (2007).
Direct positive selection for improved nitroreductase variants using SOS triggering of bacteriophage lambda lytic cycle.
  Gene Ther, 14, 690-698.  
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.  
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.  
17468253 M.St Maurice, N.Cremades, M.A.Croxen, G.Sisson, J.Sancho, and P.S.Hoffman (2007).
Flavodoxin:quinone reductase (FqrB): a redox partner of pyruvate:ferredoxin oxidoreductase that reversibly couples pyruvate oxidation to NADPH production in Helicobacter pylori and Campylobacter jejuni.
  J Bacteriol, 189, 4764-4773.  
17119634 Z.C.Symons, and N.C.Bruce (2006).
Bacterial pathways for degradation of nitroaromatics.
  Nat Prod Rep, 23, 845-850.  
16156787 H.Khan, T.Barna, N.C.Bruce, A.W.Munro, D.Leys, and N.S.Scrutton (2005).
Proton transfer in the oxidative half-reaction of pentaerythritol tetranitrate reductase. Structure of the reduced enzyme-progesterone complex and the roles of residues Tyr186, His181, His184.
  FEBS J, 272, 4660-4671.
PDB codes: 2aba 2abb
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.