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PDBsum entry 1d4c

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1d4c
Jmol
Contents
Protein chains
570 a.a. *
Ligands
HEM ×16
FAD ×4
SO4 ×3
Waters ×126
* Residue conservation analysis
PDB id:
1d4c
Name: Oxidoreductase
Title: Crystal structure of the uncomplexed form of the flavocytochromE C fumarate reductase of shewanella putrefaciens strain mr-1
Structure: FlavocytochromE C fumarate reductase. Chain: a, b, c, d. Ec: 1.3.99.1
Source: Shewanella oneidensis. Organism_taxid: 70863. Strain: mr1
Resolution:
2.90Å     R-factor:   0.210     R-free:   0.300
Authors: D.Leys,A.S.Tsapin,T.E.Meyer,M.A.Cusanovich,J.J.Van Beeumen
Key ref:
D.Leys et al. (1999). Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1. Nat Struct Biol, 6, 1113-1117. PubMed id: 10581551 DOI: 10.1038/70051
Date:
03-Oct-99     Release date:   01-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P83223  (FRDA_SHEON) -  Fumarate reductase flavoprotein subunit
Seq:
Struc:
 
Seq:
Struc:
596 a.a.
570 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.3.5.4  - Fumarate reductase (quinol).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Succinate + a quinone = fumarate + a quinol
Succinate
+ quinone
= fumarate
+ quinol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     succinate dehydrogenase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1038/70051 Nat Struct Biol 6:1113-1117 (1999)
PubMed id: 10581551  
 
 
Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.
D.Leys, A.S.Tsapin, K.H.Nealson, T.E.Meyer, M.A.Cusanovich, J.J.Van Beeumen.
 
  ABSTRACT  
 
Fumarate respiration is one of the most widespread types of anaerobic respiration. The soluble fumarate reductase of Shewanella putrefaciens MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A and 2.5 A for the fumarate and the succinate-bound protein, respectively. The structures reveal a flexible capping domain linked to the FAD-binding domain. A catalytic mechanism for fumarate reduction based on the structure of the complexed protein is proposed. The mechanism for the reverse reaction is a model for the homologous succinate dehydrogenase (complex II) of the respiratory chain. In flavocytochrome c fumarate reductase, all redox centers are in van der Waals contact with one another, thus providing an efficient conduit of electrons from the hemes via the FAD to fumarate.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Protein fold of the soluble fumarate reductase. a,b, Ribbon representation of fumarate reductase; molecule A of the orthorhombic crystal form is depicted. The cytochrome domain I is in orange and domains II, III and IV are in light blue, dark blue and green, respectively. The orientation in (b) is rotated 90° counter-clockwise horizontally and 90° clockwise along the vertical axis with respect to (a). Both figures were made using Molscript^30 and Raster3D^31. c, Superposition of the structures of fumarate reductase in the tetragonal form (green) and the orthorhombic crystal (molecule A, red; molecule D, blue) using the C coordinates of the FAD binding domain as the reference (figure generated using TURBO-FRODO^28). The view is approximately along the axis of rotation around the double hinge (see text) situated near residue 503. For clarity, only domains I, II and IV in molecule D of the orthorhombic crystal form (black lines) are shown.
Figure 3.
Figure 3. Stereo representation of the redox centers in fumarate reductase. Hemes are colored yellow (except the iron atoms, which are orange), FAD blue and the substrate green. The figure was prepared using Molscript^30 and Raster3D^31.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 1113-1117) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21419779 C.Coelho, P.J.González, J.G.Moura, I.Moura, J.Trincão, and M.João Romão (2011).
The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states.
  J Mol Biol, 408, 932-948.
PDB codes: 3ml1 3o5a
21311751 D.E.Ross, J.M.Flynn, D.B.Baron, J.A.Gralnick, and D.R.Bond (2011).
Towards electrosynthesis in shewanella: energetics of reversing the mtr pathway for reductive metabolism.
  PLoS One, 6, e16649.  
20422082 C.M.Paquete, and R.O.Louro (2010).
Molecular details of multielectron transfer: the case of multiheme cytochromes from metal respiring organisms.
  Dalton Trans, 39, 4259-4266.  
21079665 C.Marino Buslje, E.Teppa, T.Di Doménico, J.M.Delfino, and M.Nielsen (2010).
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.
  PLoS Comput Biol, 6, e1000978.  
20492688 S.K.Tai, G.Wu, S.Yuan, and K.C.Li (2010).
Genome-wide expression links the electron transfer pathway of Shewanella oneidensis to chemotaxis.
  BMC Genomics, 11, 319.  
19048308 B.M.Fonseca, I.H.Saraiva, C.M.Paquete, C.M.Soares, I.Pacheco, C.A.Salgueiro, and R.O.Louro (2009).
The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes.
  J Biol Inorg Chem, 14, 375-385.  
19170876 H.D.Juhnke, H.Hiltscher, H.R.Nasiri, H.Schwalbe, and C.R.Lancaster (2009).
Production, characterization and determination of the real catalytic properties of the putative 'succinate dehydrogenase' from Wolinella succinogenes.
  Mol Microbiol, 71, 1088-1101.  
19710024 J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, and G.Cecchini (2009).
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
  J Biol Chem, 284, 29836-29846.
PDB codes: 2wdq 2wdr 2wdv
18620418 A.S.Reger, R.Wu, D.Dunaway-Mariano, and A.M.Gulick (2008).
Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase.
  Biochemistry, 47, 8016-8025.
PDB codes: 3cw8 3cw9
18401503 M.W.van der Kamp, F.Perruccio, and A.J.Mulholland (2008).
High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase.
  Chem Commun (Camb), (), 1874-1876.  
18385138 T.M.Tomasiak, E.Maklashina, G.Cecchini, and T.M.Iverson (2008).
A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.
  J Biol Chem, 283, 15460-15468.
PDB code: 3cir
16569009 A.K.Upadhyay, A.B.Hooper, and M.P.Hendrich (2006).
NO reductase activity of the tetraheme cytochrome C554 of Nitrosomonas europaea.
  J Am Chem Soc, 128, 4330-4337.  
16484232 E.Maklashina, T.M.Iverson, Y.Sher, V.Kotlyar, J.Andréll, O.Mirza, J.M.Hudson, F.A.Armstrong, R.A.Rothery, J.H.Weiner, and G.Cecchini (2006).
Fumarate reductase and succinate oxidase activity of Escherichia coli complex II homologs are perturbed differently by mutation of the flavin binding domain.
  J Biol Chem, 281, 11357-11365.
PDB code: 2b76
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
  Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj
16699170 K.L.Pankhurst, C.G.Mowat, E.L.Rothery, J.M.Hudson, A.K.Jones, C.S.Miles, M.D.Walkinshaw, F.A.Armstrong, G.A.Reid, and S.K.Chapman (2006).
A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina.
  J Biol Chem, 281, 20589-20597.
PDB codes: 2b7r 2b7s
16935256 L.S.Huang, J.T.Shen, A.C.Wang, and E.A.Berry (2006).
Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
  Biochim Biophys Acta, 1757, 1073-1083.
PDB codes: 2h88 2h89
16234915 C.G.Mowat, and S.K.Chapman (2005).
Multi-heme cytochromes--new structures, new chemistry.
  Dalton Trans, (), 3381-3389.  
15107237 T.E.Meyer, A.I.Tsapin, I.Vandenberghe, L.de Smet, D.Frishman, K.H.Nealson, M.A.Cusanovich, and J.J.van Beeumen (2004).
Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes.
  OMICS, 8, 57-77.  
12867466 F.Reyes-Ramirez, P.Dobbin, G.Sawers, and D.J.Richardson (2003).
Characterization of transcriptional regulation of Shewanella frigidimarina Fe(III)-induced flavocytochrome c reveals a novel iron-responsive gene regulation system.
  J Bacteriol, 185, 4564-4571.  
14527321 G.Cecchini (2003).
Function and structure of complex II of the respiratory chain.
  Annu Rev Biochem, 72, 77.  
12732647 K.E.Pitts, P.S.Dobbin, F.Reyes-Ramirez, A.J.Thomson, D.J.Richardson, and H.E.Seward (2003).
Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA: expression in Escherichia coli confers the ability to reduce soluble Fe(III) chelates.
  J Biol Chem, 278, 27758-27765.  
11939777 A.Brigé, D.Leys, T.E.Meyer, M.A.Cusanovich, and J.J.Van Beeumen (2002).
The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
  Biochemistry, 41, 4827-4836.
PDB code: 1jni
12080059 D.Leys, T.E.Meyer, A.S.Tsapin, K.H.Nealson, M.A.Cusanovich, and J.J.Van Beeumen (2002).
Crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c.
  J Biol Chem, 277, 35703-35711.
PDB codes: 1m1p 1m1q 1m1r
11863440 R.T.Bossi, A.Negri, G.Tedeschi, and A.Mattevi (2002).
Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis.
  Biochemistry, 41, 3018-3024.
PDB codes: 1knp 1knr
11425747 A.I.Tsapin, I.Vandenberghe, K.H.Nealson, J.H.Scott, T.E.Meyer, M.A.Cusanovich, E.Harada, T.Kaizu, H.Akutsu, D.Leys, and J.J.Van Beeumen (2001).
Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1.
  Appl Environ Microbiol, 67, 3236-3244.  
11248702 C.R.Lancaster, R.Gross, and J.Simon (2001).
A third crystal form of Wolinella succinogenes quinol:fumarate reductase reveals domain closure at the site of fumarate reduction.
  Eur J Biochem, 268, 1820-1827.
PDB code: 1e7p
11294641 G.Tedeschi, S.Ronchi, T.Simonic, C.Treu, A.Mattevi, and A.Negri (2001).
Probing the active site of L-aspartate oxidase by site-directed mutagenesis: role of basic residues in fumarate reduction.
  Biochemistry, 40, 4738-4744.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
11004459 C.R.Lancaster, and A.Kröger (2000).
Succinate: quinone oxidoreductases: new insights from X-ray crystal structures.
  Biochim Biophys Acta, 1459, 422-431.  
11004445 G.A.Reid, C.S.Miles, R.K.Moysey, K.L.Pankhurst, and S.K.Chapman (2000).
Catalysis in fumarate reductase.
  Biochim Biophys Acta, 1459, 310-315.  
10981634 T.M.Iverson, C.Luna-Chavez, I.Schröder, G.Cecchini, and D.C.Rees (2000).
Analyzing your complexes: structure of the quinol-fumarate reductase respiratory complex.
  Curr Opin Struct Biol, 10, 448-455.  
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.