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PDBsum entry 1fqt
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Oxidoreductase PDB id
1fqt

 

 

 

 

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Contents
Protein chains
109 a.a. *
Ligands
FES ×2
GOL ×3
Waters ×314
* Residue conservation analysis
PDB id:
1fqt
Name: Oxidoreductase
Title: Crystal structure of the rieske-type ferredoxin associated with biphenyl dioxygenase
Structure: Rieske-type ferredoxin of biphenyl dioxygenase. Chain: a, b. Synonym: biphenyl dioxygenase, biphenyl dioxygenase system ferredoxin component, biphenyl dioxygenase. Engineered: yes
Source: Burkholderia xenovorans. Organism_taxid: 266265. Strain: lb400. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.180     R-free:   0.200
Authors: C.L.Colbert,M.M.-J.Couture,L.D.Eltis,J.T.Bolin
Key ref:
C.L.Colbert et al. (2000). A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins. Structure, 8, 1267-1278. PubMed id: 11188691 DOI: 10.1016/S0969-2126(00)00536-0
Date:
06-Sep-00     Release date:   03-Jan-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P37332  (BPHF_PARXL) -  Biphenyl dioxygenase system ferredoxin subunit from Paraburkholderia xenovorans (strain LB400)
Seq:
Struc: 		109 a.a.
109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.12.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0969-2126(00)00536-0 Structure 8:1267-1278 (2000)
PubMed id: 11188691  
 
 
A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins.
C.L.Colbert, M.M.Couture, L.D.Eltis, J.T.Bolin.
 
  ABSTRACT  
 
BACKGROUND: Ring-hydroxylating dioxygenases are multicomponent systems that initiate biodegradation of aromatic compounds. Many dioxygenase systems include Rieske-type ferredoxins with amino acid sequences and redox properties remarkably different from the Rieske proteins of proton-translocating clusters lie near the protein surface, operate at potentials above +300 mV at pH 7, and express pH- and ionic strength-dependent redox behavior. The reduction potentials of the dioxygenase ferredoxins are approximately 150 mV and are pH-independent. These distinctions were predicted to arise from differences in the exposure of the cluster and/or interactions of the histidine ligands. RESULTS: The crystal structure of BphF, the Rieske-type ferredoxin associated with biphenyl dioxygenase, was determined by multiwavelength anomalous diffraction and refined at 1.6 A resolution. The structure of BphF was compared with other Rieske proteins at several levels. BphF has the same two-domain fold as other Rieske proteins, but it lacks all insertions that give the others unique structural features. The BphF Fe-S cluster and its histidine ligands are exposed. However, the cluster has a significantly different environment in that five fewer polar groups interact strongly with the cluster sulfide or the cysteinyl ligands. CONCLUSIONS: BphF has structural features consistent with a minimal and perhaps archetypical Rieske protein. Variations in redox potentials among Rieske clusters appear to be largely the result of local electrostatic interactions with protein partial charges. Moreover, it appears that the redox-linked ionizations of the Rieske proteins from proton-translocating complexes are also promoted by these electrostatic interactions.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereoscopic Illustrations of the Environment of the Rieske Fe-S Center in the BphF Monomer and in the CrystalPanel (a) illustrates the cluster binding domain in monomer B. Some side chains directed away from the Fe-S cluster were truncated to improve the visibility of features nearer to the cluster. C, N, O, S, and Fe atoms are colored gray, blue, red, yellow, and red-brown, respectively. Four water molecules are plotted as violet balls. Panel (b) illustrates the environment of the cluster in the crystal. The course of portions of the backbone for two molecules related by a 2[1] screw axis are plotted in green and gold, respectively. The colors of protein and water atoms are the same as in (a). Two intermolecular hydrogen bonds are represented by dotted lines

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1267-1278) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20714442 O.Kweon, S.J.Kim, J.P.Freeman, J.Song, S.Baek, and C.E.Cerniglia (2010).
Substrate Specificity and Structural Characteristics of the Novel Rieske Nonheme Iron Aromatic Ring-Hydroxylating Oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1.
  MBio, 1, 0.  
  20885930 T.Iwasaki (2010).
Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus.
  Archaea, 2010, 0.  
19099453 D.R.Kolling, R.I.Samoilova, A.A.Shubin, A.R.Crofts, and S.A.Dikanov (2009).
Proton environment of reduced Rieske iron-sulfur cluster probed by two-dimensional ESEEM spectroscopy.
  J Phys Chem A, 113, 653-667.  
19804777 T.Iwasaki, R.I.Samoilova, A.Kounosu, and S.A.Dikanov (2009).
Two-dimensional pulsed electron spin resonance characterization of 15N-labeled archaeal Rieske-type ferredoxin.
  FEBS Lett, 583, 3467-3472.  
18766386 Y.El Khoury, and P.Hellwig (2009).
Infrared spectroscopic characterization of copper-polyhistidine from 1,800 to 50 cm(-1): model systems for copper coordination.
  J Biol Inorg Chem, 14, 23-34.  
18501698 A.R.Crofts, J.T.Holland, D.Victoria, D.R.Kolling, S.A.Dikanov, R.Gilbreth, S.Lhee, R.Kuras, and M.G.Kuras (2008).
The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex?
  Biochim Biophys Acta, 1777, 1001-1019.  
18703841 E.J.Levin, N.L.Elsen, K.D.Seder, J.G.McCoy, B.G.Fox, and G.N.Phillips (2008).
X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus.
  Acta Crystallogr D Biol Crystallogr, 64, 933-940.
PDB code: 3d89
18719951 E.N.Brown, R.Friemann, A.Karlsson, J.V.Parales, M.M.Couture, L.D.Eltis, and S.Ramaswamy (2008).
Determining Rieske cluster reduction potentials.
  J Biol Inorg Chem, 13, 1301-1313.
PDB code: 2qpz
18478354 G.M.Ullmann, E.Kloppmann, T.Essigke, E.M.Krammer, A.R.Klingen, T.Becker, and E.Bombarda (2008).
Investigating the mechanisms of photosynthetic proteins using continuum electrostatics.
  Photosynth Res, 97, 33-53.  
17992543 J.Meyer (2008).
Iron-sulfur protein folds, iron-sulfur chemistry, and evolution.
  J Biol Inorg Chem, 13, 157-170.  
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
  J Biosci Bioeng, 105, 433-449.  
19111067 R.R.Thangudu, M.Manoharan, N.Srinivasan, F.Cadet, R.Sowdhamini, and B.Offmann (2008).
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
  BMC Struct Biol, 8, 55.  
  18607094 T.Umeda, J.Katsuki, Y.Usami, K.Inoue, H.Noguchi, Z.Fujimoto, Y.Ashikawa, H.Yamane, and H.Nojiri (2008).
Crystallization and preliminary X-ray diffraction studies of a novel ferredoxin involved in the dioxygenation of carbazole by Novosphingobium sp. KA1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 632-635.  
17211635 C.L.Yu, W.Liu, D.J.Ferraro, E.N.Brown, J.V.Parales, S.Ramaswamy, G.J.Zylstra, D.T.Gibson, and R.E.Parales (2007).
Purification, characterization, and crystallization of the components of a biphenyl dioxygenase system from Sphingobium yanoikuyae B1.
  J Ind Microbiol Biotechnol, 34, 311-324.  
17349044 D.J.Ferraro, E.N.Brown, C.L.Yu, R.E.Parales, D.T.Gibson, and S.Ramaswamy (2007).
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
  BMC Struct Biol, 7, 10.
PDB codes: 2gbw 2gbx 2i7f
17223530 D.J.Kolling, J.S.Brunzelle, S.Lhee, A.R.Crofts, and S.K.Nair (2007).
Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters.
  Structure, 15, 29-38.
PDB codes: 2nuk 2num 2nve 2nvf 2nvg 2nwf
16933133 B.G.Keenan, and T.K.Wood (2006).
Orthric Rieske dioxygenases for degrading mixtures of 2,4-dinitrotoluene/naphthalene and 2-amino-4,6-dinitrotoluene/4-amino-2,6-dinitrotoluene.
  Appl Microbiol Biotechnol, 73, 827-838.  
16771672 C.M.Koehler, K.N.Beverly, and E.P.Leverich (2006).
Redox pathways of the mitochondrion.
  Antioxid Redox Signal, 8, 813-822.  
16672473 K.Inoue, H.Habe, H.Yamane, and H.Nojiri (2006).
Characterization of novel carbazole catabolism genes from gram-positive carbazole degrader Nocardioides aromaticivorans IC177.
  Appl Environ Microbiol, 72, 3321-3329.  
16627939 L.A.Moe, C.A.Bingman, G.E.Wesenberg, G.N.Phillips, and B.G.Fox (2006).
Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase.
  Acta Crystallogr D Biol Crystallogr, 62, 476-482.
PDB code: 1vm9
  16754990 M.Senda, S.Kimura, S.Kishigami, and T.Senda (2006).
Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 590-592.  
  17012793 T.Iwasaki, A.Kounosu, D.Ohmori, and T.Kumasaka (2006).
Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 993-995.  
16877714 T.Iwasaki, A.Kounosu, D.R.Kolling, S.Lhee, A.R.Crofts, S.A.Dikanov, T.Uchiyama, T.Kumasaka, H.Ishikawa, M.Kono, T.Imai, and A.Urushiyama (2006).
Resonance Raman characterization of archaeal and bacterial Rieske protein variants with modified hydrogen bond network around the [2Fe-2S] center.
  Protein Sci, 15, 2019-2024.  
15645447 J.W.Nam, H.Noguchi, Z.Fujimoto, H.Mizuno, Y.Ashikawa, M.Abo, S.Fushinobu, N.Kobashi, T.Wakagi, K.Iwata, T.Yoshida, H.Habe, H.Yamane, T.Omori, and H.Nojiri (2005).
Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system.
  Proteins, 58, 779-789.
PDB code: 1vck
15948965 S.Ouchane, W.Nitschke, P.Bianco, A.Vermeglio, and C.Astier (2005).
Multiple Rieske genes in prokaryotes: exchangeable Rieske subunits in the cytochrome bc-complex of Rubrivivax gelatinosus.
  Mol Microbiol, 57, 261-275.  
15632131 T.Iwasaki, A.Kounosu, Y.Tao, Z.Li, J.E.Shokes, N.J.Cosper, T.Imai, A.Urushiyama, and R.A.Scott (2005).
Rational design of a mononuclear metal site into the archaeal Rieske-type protein scaffold.
  J Biol Chem, 280, 9129-9134.  
14726526 A.Kounosu, Z.Li, N.J.Cosper, J.E.Shokes, R.A.Scott, T.Imai, A.Urushiyama, and T.Iwasaki (2004).
Engineering a three-cysteine, one-histidine ligand environment into a new hyperthermophilic archaeal Rieske-type [2Fe-2S] ferredoxin from Sulfolobus solfataricus.
  J Biol Chem, 279, 12519-12528.  
14977419 A.R.Crofts (2004).
The cytochrome bc1 complex: function in the context of structure.
  Annu Rev Physiol, 66, 689-733.  
15452777 L.Skjeldal, F.C.Peterson, J.F.Doreleijers, L.A.Moe, J.D.Pikus, W.M.Westler, J.L.Markley, B.F.Volkman, and B.G.Fox (2004).
Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex.
  J Biol Inorg Chem, 9, 945-953.
PDB code: 1sjg
15272185 T.Uchiyama, A.Kounosu, T.Sato, N.Tanaka, T.Iwasaki, and T.Kumasaka (2004).
Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment.
  Acta Crystallogr D Biol Crystallogr, 60, 1487-1489.  
14622010 T.Merbitz-Zahradnik, K.Zwicker, J.H.Nett, T.A.Link, and B.L.Trumpower (2003).
Elimination of the disulfide bridge in the Rieske iron-sulfur protein allows assembly of the [2Fe-2S] cluster into the Rieske protein but damages the ubiquinol oxidation site in the cytochrome bc1 complex.
  Biochemistry, 42, 13637-13645.  
14567701 Y.Zu, M.M.Couture, D.R.Kolling, A.R.Crofts, L.D.Eltis, J.A.Fee, and J.Hirst (2003).
Reduction potentials of Rieske clusters: importance of the coupling between oxidation state and histidine protonation state.
  Biochemistry, 42, 12400-12408.  
12089152 A.P.Yeh, X.I.Ambroggio, S.L.Andrade, O.Einsle, C.Chatelet, J.Meyer, and D.C.Rees (2002).
High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.
  J Biol Chem, 277, 34499-34507.
PDB codes: 1m2a 1m2b 1m2d
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.  
11967568 M.J.Maté, M.Ortiz-Lombardía, B.Boitel, A.Haouz, D.Tello, S.A.Susin, J.Penninger, G.Kroemer, and P.M.Alzari (2002).
The crystal structure of the mouse apoptosis-inducing factor AIF.
  Nat Struct Biol, 9, 442-446.
PDB code: 1gv4
12441394 N.J.Cosper, D.M.Eby, A.Kounosu, N.Kurosawa, E.L.Neidle, D.M.Kurtz, T.Iwasaki, and R.A.Scott (2002).
Redox-dependent structural changes in archaeal and bacterial Rieske-type [2Fe-2S] clusters.
  Protein Sci, 11, 2969-2973.  
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 code is shown on the right.

 

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