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PDBsum entry 1ryt
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protein metals links
Electron transport PDB id
1ryt

 

 

 

 

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Contents
Protein chain
190 a.a. *
Metals
_FE ×3
Waters ×51
* Residue conservation analysis
PDB id:
1ryt
Name: Electron transport
Title: Rubrerythrin
Structure: Rubrerythrin. Chain: a
Source: Desulfovibrio vulgaris subsp. Vulgaris str. Hildenborough. Organism_taxid: 882. Strain: hildenborough
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.10Å     R-factor:   0.182     R-free:   0.256
Authors: F.Demare,D.M.Kurtz,P.Nordlund
Key ref: F.deMaré et al. (1996). The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains. Nat Struct Biol, 3, 539-546. PubMed id: 8646540
Date:
26-Apr-96     Release date:   15-May-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24931  (RUBY_DESVH) -  Rubrerythrin from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
Seq:
Struc: 		191 a.a.
190 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Nat Struct Biol 3:539-546 (1996)
PubMed id: 8646540  
 
 
The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains.
F.deMaré, D.M.Kurtz, P.Nordlund.
 
  ABSTRACT  
 
We have determined the structure of rubrerythrin, a non-haem iron protein from the anaerobic sulphate-reducing bacterium, Desulfovibrio vulgaris (Hildenborough), by X-ray crystallography. The structure reveals a tetramer of two-domain subunits. Each subunit contains a four-helix bundle surrounding a diiron-oxo site and a C-terminal rubredoxin-like FeS4 domain. The diiron-oxo site contains a larger number of carboxylate ligands and a higher degree of solvent exposure than do those in other diiron-oxo proteins. The four-helix bundle of rubrerythrin closely resembles those of the ferritin and bacterioferritin subunits, suggesting a relationship among these proteins-consistent with the recently demonstrated ferroxidase activity of rubrerythrin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21170562 A.F.Pinto, S.Todorovic, P.Hildebrandt, M.Yamazaki, F.Amano, S.Igimi, C.V.Romão, and M.Teixeira (2011).
Desulforubrerythrin from Campylobacter jejuni, a novel multidomain protein.
  J Biol Inorg Chem, 16, 501-510.  
20159152 Y.Luo, C.E.Ergenekan, J.T.Fischer, M.L.Tan, and T.Ichiye (2010).
The molecular determinants of the increased reduction potential of the rubredoxin domain of rubrerythrin relative to rubredoxin.
  Biophys J, 98, 560-568.  
19759909 W.S.Maaty, B.Wiedenheft, P.Tarlykov, N.Schaff, J.Heinemann, J.Robison-Cox, J.Valenzuela, A.Dougherty, P.Blum, C.M.Lawrence, T.Douglas, M.J.Young, and B.Bothner (2009).
Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress.
  PLoS One, 4, e6964.  
18400177 A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, and B.L.Stoddard (2008).
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.
  Structure, 16, 558-569.
PDB codes: 3bvq 3c25
17992543 J.Meyer (2008).
Iron-sulfur protein folds, iron-sulfur chemistry, and evolution.
  J Biol Inorg Chem, 13, 157-170.  
18021800 M.Proudfoot, S.A.Sanders, A.Singer, R.Zhang, G.Brown, A.Binkowski, L.Xu, J.A.Lukin, A.G.Murzin, A.Joachimiak, C.H.Arrowsmith, A.M.Edwards, A.V.Savchenko, and A.F.Yakunin (2008).
Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain.
  J Mol Biol, 375, 301-315.
PDB codes: 1pvm 2qh1
17001035 A.Hindupur, D.Liu, Y.Zhao, H.D.Bellamy, M.A.White, and R.O.Fox (2006).
The crystal structure of the E. coli stress protein YciF.
  Protein Sci, 15, 2605-2611.
PDB code: 2gs4
16463182 F.Hillmann, R.J.Fischer, and H.Bahl (2006).
The rubrerythrin-like protein Hsp21 of Clostridium acetobutylicum is a general stress protein.
  Arch Microbiol, 185, 270-276.  
17176061 M.H.Sazinsky, P.W.Dunten, M.S.McCormick, A.DiDonato, and S.J.Lippard (2006).
X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase.
  Biochemistry, 45, 15392-15404.
PDB codes: 2inn 2inp
16605252 P.Sobrado, K.S.Lyle, S.P.Kaul, M.M.Turco, I.Arabshahi, A.Marwah, and B.G.Fox (2006).
Identification of the binding region of the [2Fe-2S] ferredoxin in stearoyl-acyl carrier protein desaturase: insight into the catalytic complex and mechanism of action.
  Biochemistry, 45, 4848-4858.  
16084393 I.Friedberg, and A.Godzik (2005).
Connecting the protein structure universe by using sparse recurring fragments.
  Structure, 13, 1213-1224.  
16100392 J.B.Vicente, and M.Teixeira (2005).
Redox and spectroscopic properties of the Escherichia coli nitric oxide-detoxifying system involving flavorubredoxin and its NADH-oxidizing redox partner.
  J Biol Chem, 280, 34599-34608.  
15700297 J.R.Calhoun, F.Nastri, O.Maglio, V.Pavone, A.Lombardi, and W.F.DeGrado (2005).
Artificial diiron proteins: from structure to function.
  Biopolymers, 80, 264-278.  
15895271 R.B.Iyer, R.Silaghi-Dumitrescu, D.M.Kurtz, and W.N.Lanzilotta (2005).
High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins.
  J Biol Inorg Chem, 10, 407-416.
PDB codes: 1yux 1yuz 1yv1
16301793 R.E.Stenkamp (2005).
Anatomy of a trans-cis peptide transition during least-squares refinement of rubrerythrin.
  Acta Crystallogr D Biol Crystallogr, 61, 1599-1602.  
15336429 A.May, F.Hillmann, O.Riebe, R.J.Fischer, and H.Bahl (2004).
A rubrerythrin-like oxidative stress protein of Clostridium acetobutylicum is encoded by a duplicated gene and identical to the heat shock protein Hsp21.
  FEMS Microbiol Lett, 238, 249-254.  
15547260 M.V.Weinberg, F.E.Jenney, X.Cui, and M.W.Adams (2004).
Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase.
  J Bacteriol, 186, 7888-7895.  
15158262 M.Yamasaki, S.Igimi, Y.Katayama, S.Yamamoto, and F.Amano (2004).
Identification of an oxidative stress-sensitive protein from Campylobacter jejuni, homologous to rubredoxin oxidoreductase/rubrerythrin.
  FEMS Microbiol Lett, 235, 57-63.  
15468318 W.Tempel, Z.J.Liu, F.D.Schubot, A.Shah, M.V.Weinberg, F.E.Jenney, W.B.Arendall, M.W.Adams, J.S.Richardson, D.C.Richardson, J.P.Rose, and B.C.Wang (2004).
Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin.
  Proteins, 57, 878-882.
PDB code: 1nnq
12655046 D.T.Logan, E.Mulliez, K.M.Larsson, S.Bodevin, M.Atta, P.E.Garnaud, B.M.Sjoberg, and M.Fontecave (2003).
A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase.
  Proc Natl Acad Sci U S A, 100, 3826-3831.
PDB code: 1hk8
12727864 M.A.Carrondo (2003).
Ferritins, iron uptake and storage from the bacterioferritin viewpoint.
  EMBO J, 22, 1959-1968.  
12704186 M.Moche, J.Shanklin, A.Ghoshal, and Y.Lindqvist (2003).
Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.
  J Biol Chem, 278, 25072-25080.
PDB codes: 1oq4 1oq7 1oq9 1oqb
12730190 T.J.Stillman, P.P.Connolly, C.L.Latimer, A.F.Morland, M.A.Quail, S.C.Andrews, A.Treffry, J.R.Guest, P.J.Artymiuk, and P.M.Harrison (2003).
Insights into the effects on metal binding of the systematic substitution of five key glutamate ligands in the ferritin of Escherichia coli.
  J Biol Chem, 278, 26275-26286.  
12757943 T.Wakagi (2003).
Sulerythrin, the smallest member of the rubrerythrin family, from a strictly aerobic and thermoacidophilic archaeon, Sulfolobus tokodaii strain 7.
  FEMS Microbiol Lett, 222, 33-37.  
11972784 M.Sztukowska, M.Bugno, J.Potempa, J.Travis, and D.M.Kurtz (2002).
Role of rubrerythrin in the oxidative stress response of Porphyromonas gingivalis.
  Mol Microbiol, 44, 479-488.  
11828492 C.M.Gomes, J.Le Gall, A.V.Xavier, and M.Teixeira (2001).
Could a diiron-containing four-helix-bundle protein have been a primitive oxygen reductase?
  Chembiochem, 2, 583-587.  
11114906 H.L.Lumppio, N.V.Shenvi, A.O.Summers, G.Voordouw, and D.M.Kurtz (2001).
Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system.
  J Bacteriol, 183, 101-108.  
10841536 A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, and W.F.DeGrado (2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
  Proc Natl Acad Sci U S A, 97, 6298-6305.
PDB code: 1ec5
11106766 D.A.Berthold, M.E.Andersson, and P.Nordlund (2000).
New insight into the structure and function of the alternative oxidase.
  Biochim Biophys Acta, 1460, 241-254.  
  10493590 B.R.Gibney, and P.L.Dutton (1999).
Histidine placement in de novo-designed heme proteins.
  Protein Sci, 8, 1888-1898.  
10449377 C.M.Summa, A.Lombardi, M.Lewis, and W.F.DeGrado (1999).
Tertiary templates for the design of diiron proteins.
  Curr Opin Struct Biol, 9, 500-508.  
  10422844 M.Archer, A.L.Carvalho, S.Teixeira, I.Moura, J.J.Moura, F.Rusnak, and M.J.Romão (1999).
Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein.
  Protein Sci, 8, 1536-1545.
PDB codes: 1cfw 1dcd 1dhg
10555962 M.K.Eidsness, A.E.Burden, K.A.Richie, D.M.Kurtz, R.A.Scott, E.T.Smith, T.Ichiye, B.Beard, T.Min, and C.Kang (1999).
Modulation of the redox potential of the [Fe(SCys)(4)] site in rubredoxin by the orientation of a peptide dipole.
  Biochemistry, 38, 14803-14809.
PDB code: 1c09
9692970 D.T.Logan, F.deMaré, B.O.Persson, A.Slaby, B.M.Sjöberg, and P.Nordlund (1998).
Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins.
  Biochemistry, 37, 10798-10807.
PDB code: 1biq
9852763 J.Stubbe, and P.Riggs-Gelasco (1998).
Harnessing free radicals: formation and function of the tyrosyl radical in ribonucleotide reductase.
  Trends Biochem Sci, 23, 438-443.  
9546221 R.A.Grant, D.J.Filman, S.E.Finkel, R.Kolter, and J.M.Hogle (1998).
The crystal structure of Dps, a ferritin homolog that binds and protects DNA.
  Nat Struct Biol, 5, 294-303.
PDB code: 1dps
  9226272 H.L.Lumppio, N.V.Shenvi, R.P.Garg, A.O.Summers, and D.M.Kurtz (1997).
A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough).
  J Bacteriol, 179, 4607-4615.  
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.

 

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