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PDBsum entry 1bcf
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protein ligands metals Protein-protein interface(s) links
Iron storage and electron transport PDB id
1bcf

 

 

 

 

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Contents
Protein chains
(+ 6 more) 158 a.a. *
Ligands
HEM ×6
Metals
_MN ×24
* Residue conservation analysis
PDB id:
1bcf
Name: Iron storage and electron transport
Title: The structure of a unique, two-fold symmetric, haem-binding site
Structure: Bacterioferritin. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: 24mer (from PQS)
Resolution:
2.90Å     R-factor:   0.208    
Authors: F.Frolow,A.J.Kalb(gilboa),J.Yariv
Key ref: F.Frolow et al. (1994). Structure of a unique twofold symmetric haem-binding site. Nat Struct Biol, 1, 453-460. PubMed id: 7664064
Date:
06-Dec-93     Release date:   20-Dec-94    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ABD3  (BFR_ECOLI) -  Bacterioferritin from Escherichia coli (strain K12)
Seq:
Struc: 		158 a.a.
158 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.16.3.1  - ferroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 Fe2+ + O2 + 4 H+ = 4 Fe3+ + 2 H2O
4 × Fe(2+)
 + O2
 + 4 × H(+)
 = 4 × Fe(3+)
 + 2 × H2O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
Nat Struct Biol 1:453-460 (1994)
PubMed id: 7664064  
 
 
Structure of a unique twofold symmetric haem-binding site.
F.Frolow, A.J.Kalb, J.Yariv.
 
  ABSTRACT  
 
Bacterioferritin of Escherichia coli, also known as cytochrome b1, is a hollow, nearly spherical shell made up of 24 identical protein subunits and 12 haems. We have solved this structure in a tetragonal crystal form at 2.9 A resolution. We find that each haem is bound in a pocket formed by the interface between a pair of symmetry-related subunits. The quasi-twofold axis of the haem is closely aligned with the local twofold axis relating these subunits. The axial ligands of the haem are sulphurs of two equivalent methionyl residues (Met 52) from the symmetry-related subunits. A cluster of four water molecules is trapped in the gap between the upper edge of the haem and two extended protein loops which close off the haem from the outer aqueous environment. This is the first structure of a bis-methionine ligated haem-binding site and the first case of a twofold symmetric haem-binding site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20225070 R.Torres Martin de Rosales, M.Faiella, E.Farquhar, L.Que, C.Andreozzi, V.Pavone, O.Maglio, F.Nastri, and A.Lombardi (2010).
Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions.
  J Biol Inorg Chem, 15, 717-728.  
20007325 T.Masuda, F.Goto, T.Yoshihara, and B.Mikami (2010).
Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin.
  J Biol Chem, 285, 4049-4059.
PDB codes: 3a68 3a9q
18946693 S.C.Willies, M.N.Isupov, E.F.Garman, and J.A.Littlechild (2009).
The binding of haem and zinc in the 1.9 A X-ray structure of Escherichia coli bacterioferritin.
  J Biol Inorg Chem, 14, 201-207.
PDB code: 2vxi
19439409 S.G.Wong, S.A.Tom-Yew, A.Lewin, N.E.Le Brun, G.R.Moore, M.E.Murphy, and A.G.Mauk (2009).
Structural and Mechanistic Studies of a Stabilized Subunit Dimer Variant of Escherichia coli Bacterioferritin Identify Residues Required for Core Formation.
  J Biol Chem, 284, 18873-18881.
PDB code: 3e2c
19946376 V.Gupta, R.K.Gupta, G.Khare, D.M.Salunke, and A.K.Tyagi (2009).
Crystal structure of Bfr A from Mycobacterium tuberculosis: incorporation of selenomethionine results in cleavage and demetallation of haem.
  PLoS One, 4, e8028.
PDB code: 2wtl
18777102 B.Conlan (2008).
Designing photosystem II: molecular engineering of photo-catalytic proteins.
  Photosynth Res, 98, 687-700.  
19025650 H.Osorio, V.Martinez, P.A.Nieto, D.S.Holmes, and R.Quatrini (2008).
Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility.
  BMC Microbiol, 8, 203.  
18445621 R.Janowski, T.Auerbach-Nevo, and M.S.Weiss (2008).
Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site.
  Protein Sci, 17, 1138-1150.
PDB code: 3bkn
19011101 T.Tosha, M.R.Hasan, and E.C.Theil (2008).
The ferritin Fe2 site at the diiron catalytic center controls the reaction with O2 in the rapid mineralization pathway.
  Proc Natl Acad Sci U S A, 105, 18182-18187.  
17920629 R.Aranda, C.E.Worley, M.Liu, E.Bitto, M.S.Cates, J.S.Olson, B.Lei, and G.N.Phillips (2007).
Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp.
  J Mol Biol, 374, 374-383.
PDB code: 2q7a
17955341 T.Wydrzynski, W.Hillier, and B.Conlan (2007).
Engineering model proteins for Photosystem II function.
  Photosynth Res, 94, 225-233.  
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
  17077480 A.van Eerde, S.Wolterink-van Loo, J.van der Oost, and B.W.Dijkstra (2006).
Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1061-1066.
PDB code: 2htn
16855817 C.V.Romão, E.P.Mitchell, and S.McSweeney (2006).
The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus.
  J Biol Inorg Chem, 11, 891-902.
PDB codes: 2c2f 2c2u
16953567 G.H.Gauss, P.Benas, B.Wiedenheft, M.Young, T.Douglas, and C.M.Lawrence (2006).
Structure of the DPS-like protein from Sulfolobus solfataricus reveals a bacterioferritin-like dimetal binding site within a DPS-like dodecameric assembly.
  Biochemistry, 45, 10815-10827.
PDB code: 2clb
16341820 J.Tatur, P.L.Hagedoorn, M.L.Overeijnder, and W.R.Hagen (2006).
A highly thermostable ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus.
  Extremophiles, 10, 139-148.  
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
16428284 S.Sacquin-Mora, and R.Lavery (2006).
Investigating the local flexibility of functional residues in hemoproteins.
  Biophys J, 90, 2706-2717.  
16258608 A.Lewin, G.R.Moore, and N.E.Le Brun (2005).
Formation of protein-coated iron minerals.
  Dalton Trans, (), 3597-3610.  
15652979 T.Olczak, W.Simpson, X.Liu, and C.A.Genco (2005).
Iron and heme utilization in Porphyromonas gingivalis.
  FEMS Microbiol Rev, 29, 119-144.  
12727864 M.A.Carrondo (2003).
Ferritins, iron uptake and storage from the bacterioferritin viewpoint.
  EMBO J, 22, 1959-1968.  
12876316 M.A.Kilic, S.Spiro, and G.R.Moore (2003).
Stability of a 24-meric homopolymer: comparative studies of assembly-defective mutants of Rhodobacter capsulatus bacterioferritin and the native protein.
  Protein Sci, 12, 1663-1674.  
12655072 O.Maglio, F.Nastri, V.Pavone, A.Lombardi, and W.F.DeGrado (2003).
Preorganization of molecular binding sites in designed diiron proteins.
  Proc Natl Acad Sci U S A, 100, 3772-3777.
PDB code: 1nvo
12627224 S.Macedo, C.V.Romão, E.Mitchell, P.M.Matias, M.Y.Liu, A.V.Xavier, J.LeGall, M.Teixeira, P.Lindley, and M.A.Carrondo (2003).
The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans.
  Nat Struct Biol, 10, 285-290.
PDB codes: 1nf4 1nf6 1nfv
11959963 E.N.Marsh, and W.F.DeGrado (2002).
Noncovalent self-assembly of a heterotetrameric diiron protein.
  Proc Natl Acad Sci U S A, 99, 5150-5154.  
11454214 P.N.da Costa, C.V.Romão, J.LeGall, A.V.Xavier, E.Melo, M.Teixeira, and L.M.Saraiva (2001).
The genetic organization of Desulfovibrio desulphuricans ATCC 27774 bacterioferritin and rubredoxin-2 genes: involvement of rubredoxin in iron metabolism.
  Mol Microbiol, 41, 217-227.  
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
10841764 C.V.Romåo, M.Regalla, A.V.Xavier, M.Teixeira, M.Y.Liu, and J.Le Gall (2000).
A bacterioferritin from the strict anaerobe Desulfovibrio desulfuricans ATCC 27774.
  Biochemistry, 39, 6841-6849.  
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.  
  10866831 T.Mizobata, M.Kagawa, N.Murakoshi, E.Kusaka, K.Kameo, Y.Kawata, and J.Nagai (2000).
Overproduction of Thermus sp. YS 8-13 manganese catalase in Escherichia coli production of soluble apoenzyme and in vitro formation of active holoenzyme.
  Eur J Biochem, 267, 4264-4271.  
  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.  
10387019 E.R.Bauminger, A.Treffry, M.A.Quail, Z.Zhao, I.Nowik, and P.M.Harrison (1999).
Stages in iron storage in the ferritin of Escherichia coli (EcFtnA): analysis of Mössbauer spectra reveals a new intermediate.
  Biochemistry, 38, 7791-7802.  
10564468 F.Tonello, W.G.Dundon, B.Satin, M.Molinari, G.Tognon, G.Grandi, G.Del Giudice, R.Rappuoli, and C.Montecucco (1999).
The Helicobacter pylori neutrophil-activating protein is an iron-binding protein with dodecameric structure.
  Mol Microbiol, 34, 238-246.  
  10368148 J.F.Ma, U.A.Ochsner, M.G.Klotz, V.K.Nanayakkara, M.L.Howell, Z.Johnson, J.E.Posey, M.L.Vasil, J.J.Monaco, and D.J.Hassett (1999).
Bacterioferritin A modulates catalase A (KatA) activity and resistance to hydrogen peroxide in Pseudomonas aeruginosa.
  J Bacteriol, 181, 3730-3742.  
10194323 J.L.Johnson, D.C.Norcross, P.Arosio, R.B.Frankel, and G.D.Watt (1999).
Redox reactivity of animal apoferritins and apoheteropolymers assembled from recombinant heavy and light human chain ferritins.
  Biochemistry, 38, 4089-4096.  
9687369 A.C.Martin, C.A.Orengo, E.G.Hutchinson, S.Jones, M.Karmirantzou, R.A.Laskowski, J.B.Mitchell, C.Taroni, and J.M.Thornton (1998).
Protein folds and functions.
  Structure, 6, 875-884.  
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
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
8995278 A.M.Keech, N.E.Le Brun, M.T.Wilson, S.C.Andrews, G.R.Moore, and A.J.Thomson (1997).
Spectroscopic studies of cobalt(II) binding to Escherichia coli bacterioferritin.
  J Biol Chem, 272, 422-429.  
9409768 L.E.Bertani, J.S.Huang, B.A.Weir, and J.L.Kirschvink (1997).
Evidence for two types of subunits in the bacterioferritin of Magnetospirillum magnetotacticum.
  Gene, 201, 31-36.  
  9317046 P.A.Denoel, R.M.Crawford, M.S.Zygmunt, A.Tibor, V.E.Weynants, F.Godfroid, D.L.Hoover, and J.J.Letesson (1997).
Survival of a bacterioferritin deletion mutant of Brucella melitensis 16M in human monocyte-derived macrophages.
  Infect Immun, 65, 4337-4340.  
8674981 C.N.Penfold, P.L.Ringeling, S.L.Davy, G.R.Moore, A.G.McEwan, and S.Spiro (1996).
Isolation, characterisation and expression of the bacterioferritin gene of Rhodobacter capsulatus.
  FEMS Microbiol Lett, 139, 143-148.  
8695634 P.M.Harrison, and P.Arosio (1996).
The ferritins: molecular properties, iron storage function and cellular regulation.
  Biochim Biophys Acta, 1275, 161-203.  
8639572 R.P.Garg, C.J.Vargo, X.Cui, and D.M.Kurtz (1996).
A [2Fe-2S] protein encoded by an open reading frame upstream of the Escherichia coli bacterioferritin gene.
  Biochemistry, 35, 6297-6301.  
8749363 P.Nordlund, and H.Eklund (1995).
Di-iron-carboxylate proteins.
  Curr Opin Struct Biol, 5, 758-766.  
7559480 S.C.Andrews, N.E.Le Brun, V.Barynin, A.J.Thomson, G.R.Moore, J.R.Guest, and P.M.Harrison (1995).
Site-directed replacement of the coaxial heme ligands of bacterioferritin generates heme-free variants.
  J Biol Chem, 270, 23268-23274.  
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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