PDBsum entry 1krh

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Oxidoreductase PDB id
Jmol PyMol
Protein chains
337 a.a. *
SO4 ×5
FES ×2
FAD ×2
Waters ×364
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: X-ray structure of benzoate dioxygenase reductase
Structure: Benzoate 1,2-dioxygenase reductase. Chain: a, b. Engineered: yes
Source: Acinetobacter sp.. Organism_taxid: 472. Gene: benc. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.50Å     R-factor:   0.242     R-free:   0.249
Authors: A.Karlsson,Z.M.Beharry,D.M.Eby,E.D.Coulter,E.L.Niedle,D.M.Ku H.Eklund,S.Ramaswamy
Key ref:
A.Karlsson et al. (2002). X-ray crystal structure of benzoate 1,2-dioxygenase reductase from Acinetobacter sp. strain ADP1. J Mol Biol, 318, 261-272. PubMed id: 12051836 DOI: 10.1016/S0022-2836(02)00039-6
09-Jan-02     Release date:   15-May-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07771  (BENC_ACIAD) -  Benzoate 1,2-dioxygenase electron transfer component
348 a.a.
337 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.  - Ferredoxin--NAD(+) reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Reduced ferredoxin + NAD+ = oxidized ferredoxin + NADH
Reduced ferredoxin
+ NAD(+)
= oxidized ferredoxin
      Cofactor: FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     electron carrier activity     6 terms  


DOI no: 10.1016/S0022-2836(02)00039-6 J Mol Biol 318:261-272 (2002)
PubMed id: 12051836  
X-ray crystal structure of benzoate 1,2-dioxygenase reductase from Acinetobacter sp. strain ADP1.
A.Karlsson, Z.M.Beharry, D.Matthew Eby, E.D.Coulter, E.L.Neidle, D.M.Kurtz, H.Eklund, S.Ramaswamy.
One of the major processes for aerobic biodegradation of aromatic compounds is initiated by Rieske dioxygenases. Benzoate dioxygenase contains a reductase component, BenC, that is responsible for the two-electron transfer from NADH via FAD and an iron-sulfur cluster to the terminal oxygenase component. Here, we present the structure of BenC from Acinetobacter sp. strain ADP1 at 1.5 A resolution. BenC contains three domains, each binding a redox cofactor: iron-sulfur, FAD and NADH, respectively. The [2Fe-2S] domain is similar to that of plant ferredoxins, and the FAD and NADH domains are similar to members of the ferredoxin:NADPH reductase superfamily. In phthalate dioxygenase reductase, the only other Rieske dioxygenase reductase for which a crystal structure is available, the ferredoxin-like and flavin binding domains are sequentially reversed compared to BenC. The BenC structure shows significant differences in the location of the ferredoxin domain relative to the other domains, compared to phthalate dioxygenase reductase and other known systems containing these three domains. In BenC, the ferredoxin domain interacts with both the flavin and NAD(P)H domains. The iron-sulfur center and the flavin are about 9 A apart, which allows a fast electron transfer. The BenC structure is the first determined for a reductase from the class IB Rieske dioxygenases, whose reductases transfer electrons directly to their oxygenase components. Based on sequence similarities, a very similar structure was modeled for the class III naphthalene dioxygenase reductase, which transfers electrons to an intermediary ferredoxin, rather than the oxygenase component.
  Selected figure(s)  
Figure 3.
Figure 3. Stereo representation of the [2Fe-2S] center in BenC. The center is connected to the protein via cysteine residues 41, 46, 49 and 83, which ligate the two iron atoms as well as by an intricate hydrogen bonding pattern, represented by broken red lines, to the cysteine sulfur atoms and bridging sulfides.
Figure 4.
Figure 4. FAD binding in BenC. (a) The FAD-binding site is situated between the FAD-binding domain, in yellow, and the NADH-binding domain, in blue. The methyl groups of the isoalloxazine ring are pointing towards the [2Fe-2S] center in the ferredoxin-like domain. The FAD is represented inside a F[o] -F[c] map, colored in green, contoured at 4×rms. The picture was made with the program BOBSCRIPT ( (b) A close-up of the FAD molecule binding to the NADH and FAD binding domains of BenC. There are five water molecules contributing to the extensive hydrogen bonding holding the FAD in position. The stacking interaction between Phe335 and the isoalloxazine ring of the FAD can be seen at the bottom right of the Figure.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 261-272) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19708087 N.Shibata, Y.Ueda, D.Takeuchi, Y.Haruyama, S.Kojima, J.Sato, Y.Niimura, M.Kitamura, and Y.Higuchi (2009).
Structure analysis of the flavoredoxin from Desulfovibrio vulgaris Miyazaki F reveals key residues that discriminate the functions and properties of the flavin reductase family.
  FEBS J, 276, 4840-4853.  
17964805 L.J.Bailey, N.L.Elsen, B.S.Pierce, and B.G.Fox (2008).
Soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase.
  Protein Expr Purif, 57, 9.  
17567152 M.B.Neibergall, A.Stubna, Y.Mekmouche, E.Münck, and J.D.Lipscomb (2007).
Hydrogen peroxide dependent cis-dihydroxylation of benzoate by fully oxidized benzoate 1,2-dioxygenase.
  Biochemistry, 46, 8004-8016.  
  17554172 Y.Ashikawa, H.Uchimura, Z.Fujimoto, K.Inoue, H.Noguchi, H.Yamane, and H.Nojiri (2007).
Crystallization and preliminary X-ray diffraction studies of the ferredoxin reductase component in the Rieske nonhaem iron oxygenase system carbazole 1,9a-dioxygenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 499-502.  
17087501 Y.Chang, and B.G.Fox (2006).
Identification of Rv3230c as the NADPH oxidoreductase of a two-protein DesA3 acyl-CoA desaturase in Mycobacterium tuberculosis H37Rv.
  Biochemistry, 45, 13476-13486.  
14613937 J.L.Blazyk, and S.J.Lippard (2004).
Domain engineering of the reductase component of soluble methane monooxygenase from Methylococcus capsulatus (Bath).
  J Biol Chem, 279, 5630-5640.  
15010474 K.Türk, A.Puhar, F.Neese, E.Bill, G.Fritz, and J.Steuber (2004).
NADH oxidation by the Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae: functional role of the NqrF subunit.
  J Biol Chem, 279, 21349-21355.  
14622009 Z.M.Beharry, D.M.Eby, E.D.Coulter, R.Viswanathan, E.L.Neidle, R.S.Phillips, and D.M.Kurtz (2003).
Histidine ligand protonation and redox potential in the rieske dioxygenases: role of a conserved aspartate in anthranilate 1,2-dioxygenase.
  Biochemistry, 42, 13625-13636.  
12450807 J.W.Nam, H.Nojiri, H.Noguchi, H.Uchimura, T.Yoshida, H.Habe, H.Yamane, and T.Omori (2002).
Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10.
  Appl Environ Microbiol, 68, 5882-5890.  
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.