P0ABD3 (BFR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bacterioferritin
Short name=BFR
EC=1.16.3.1

Alternative name(s):
Cytochrome b-1
Cytochrome b-557

Gene names

Name:	bfr
Ordered Locus Names:	b3336, JW3298

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	158 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Iron-storage protein, whose ferroxidase center binds Fe2+ ions, oxidizes them by dioxygen to Fe3+, and participates in the subsequent Fe3+ oxide mineral core formation within the central cavity of the protein complex. The mineralized iron core can contain as many as 2700 iron atoms/24-meric molecule. Ref.8 Ref.9
Catalytic activity	4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O. Ref.8 Ref.9 Ref.13
Cofactor	Binds 1 heme B (iron-protoporphyrin IX) group per dimer. Ref.7 Ref.14 Binds 2 iron ions per subunit. The catalytic dinuclear iron-binding site within each subunit is known as the ferroxidase center. In BFR, the ferroxidase center appears to function as a true di-iron catalytic cofactor, rather than as a pore for the transfer of iron into the central cavity, as found for eukaryotic ferritins. Ref.14
Enzyme regulation	Iron oxidation is inhibited by Zn2+, which binds at the ferroxidase center with a higher affinity that Fe2+. The occupation of the ferroxidase center by Zn2+ also severely restricts the ability of BFR to form an iron core. Ref.8 Ref.9 Ref.13
Subunit structure	Homooligomer of 24 subunits, arranged as 12 dimers, that are packed together to form an approximately spherical molecule with a central cavity, in which large amounts of iron can be deposited as a ferric-oxy-hydroxide mineral core. Ref.11
Miscellaneous	The internal surface iron site that binds iron 3 is important for the mineralization phase but not for Fe2+ binding and oxidation at the ferroxidase center.
Sequence similarities	Belongs to the bacterioferritin family. Contains 1 ferritin-like diiron domain.
Mass spectrometry	Molecular mass is 18496±2 Da from positions 1 - 158. Determined by ESI. Ref.7

Ontologies

Keywords
Biological process	Iron storage
Ligand	Heme Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	cellular iron ion homeostasis Inferred from electronic annotation. Source: UniProtKB-KW iron ion transport Inferred from electronic annotation. Source: InterPro
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	ferric iron binding Inferred from electronic annotation. Source: InterPro ferroxidase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 158

158

Bacterioferritin

PRO_0000192592

Regions

Domain

1 – 145

145

Ferritin-like diiron

Sites

Metal binding

18

1

Iron 1

Metal binding

46

1

Iron 3

Metal binding

50

1

Iron 3

Metal binding

51

1

Iron 1

Metal binding

51

1

Iron 2

Metal binding

52

1

Iron (heme axial ligand); shared with dimeric partner

Metal binding

54

1

Iron 1

Metal binding

94

1

Iron 2

Metal binding

127

1

Iron 1

Metal binding

127

1

Iron 2

Metal binding

130

1

Iron 2

Natural variations

Natural variant

5 – 7

3

TKV → VKI in strain: ECOR 30.

Natural variant

38

1

K → M in strain: ECOR 30.

Natural variant

57

1

R → K in strain: ECOR 30.

Natural variant

68

1

L → I in strain: ECOR 30.

Natural variant

78

1

N → G in strain: ECOR 30.

Natural variant

88

1

R → Q in strain: ECOR 30.

Natural variant

92

1

A → R in strain: ECOR 30.

Natural variant

96

1

D → E in strain: ECOR 30.

Natural variant

100

1

N → D in strain: ECOR 30.

Natural variant

106

1

G → A in strain: ECOR 30.

Natural variant

125

1

R → A in strain: ECOR 30.

Natural variant

142 – 144

3

QKM → GKI in strain: ECOR 30.

Natural variant

152 – 158

7

AQIREEG → SQIKVKD in strain: ECOR 30.

Experimental info

Mutagenesis

18

1

E → A: Highly decreased Fe(2+) oxidation activity. Is also severely restricted in its ability to lay down an iron core. Ref.9

Mutagenesis

31

1

M → H or L: No loss of heme binding. Ref.7

Mutagenesis

46

1

H → A: Fe(2+)-binding and single turnover oxidation at the ferroxidase center occur normally but iron mineralization within the cavity is significantly impaired. Ref.14

Mutagenesis

50

1

D → A: Fe(2+)-binding and single turnover oxidation at the ferroxidase center occur normally but iron mineralization within the cavity is significantly impaired. Ref.14

Mutagenesis

52

1

M → H or L: Loss of heme binding. Is still capable of accumulating iron. Ref.7

Mutagenesis

86

1

M → L: No loss of heme binding. Ref.7

Mutagenesis

127

1

E → Q: Decreased Fe(2+) oxidation activity. Is also affected in its ability to lay down an iron core. Ref.9

Mutagenesis

130

1

H → E: Decreased Fe(2+) oxidation activity. Is also severely restricted in its ability to lay down an iron core. Ref.9

Sequence conflict

53

1

K → M AA sequence Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

158

Helix Strand Turn

Details...

Helix

5 – 35

31

Helix

38 – 64

27

Helix

83 – 111

29

Helix

114 – 144

31

Helix

146 – 151

6

Sequences

	Sequence		Length	Mass (Da)
	P0ABD3 [UniParc]. Last modified October 25, 2005. Version 1. Checksum: A6C86CE1CD8F865A	FASTA	158	18,495
	10 20 30 40 50 60 MKGDTKVINY LNKLLGNELV AINQYFLHAR MFKNWGLKRL NDVEYHESID EMKHADRYIE 70 80 90 100 110 120 RILFLEGLPN LQDLGKLNIG EDVEEMLRSD LALELDGAKN LREAIGYADS VHDYVSRDMM 130 140 150 IEILRDEEGH IDWLETELDL IQKMGLQNYL QAQIREEG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, sequencing, and mapping of the bacterioferritin gene (bfr) of Escherichia coli K-12." Andrews S.C., Harrison P.M., Guest J.R. J. Bacteriol. 171:3940-3947(1989) [PubMed: 2661540] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	Noorani S.M., Lindahl L., Zengel J.M. Submitted (APR-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ECOR 30.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Amino acid sequence of the bacterioferritin (cytochrome b1) of Escherichia coli-K12." Andrews S.C., Smith J.M.A., Guest J.R., Harrison P.M. Biochem. Biophys. Res. Commun. 158:489-496(1989) [PubMed: 2644932] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-87. Strain: K12.
[6]	"Escherichia coli contains a set of genes homologous to those involved in protein secretion, DNA uptake and the assembly of type-4 fimbriae in other bacteria." Whitchurch C.B., Mattick J.S. Gene 150:9-15(1994) [PubMed: 7959070] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 128-158. Strain: K12.
[7]	"Site-directed replacement of the coaxial heme ligands of bacterioferritin generates heme-free variants." Andrews S.C., Le Brun N.E., Barynin V., Thomson A.J., Moore G.R., Guest J.R., Harrison P.M. J. Biol. Chem. 270:23268-23274(1995) [PubMed: 7559480] [Abstract] Cited for: HEME-BINDING, MASS SPECTROMETRY, MUTAGENESIS OF MET-31; MET-52 AND MET-86. Strain: K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926.
[8]	"The iron oxidation and hydrolysis chemistry of Escherichia coli bacterioferritin." Yang X., Le Brun N.E., Thomson A.J., Moore G.R., Chasteen N.D. Biochemistry 39:4915-4923(2000) [PubMed: 10769150] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION.
[9]	"Core formation in Escherichia coli bacterioferritin requires a functional ferroxidase center." Baaghil S., Lewin A., Moore G.R., Le Brun N.E. Biochemistry 42:14047-14056(2003) [PubMed: 14636073] [Abstract] Cited for: FUNCTION, ROLE OF THE FERROXIDASE CENTER IN CORE FORMATION, CATALYTIC ACTIVITY, ENZYME REGULATION, MUTAGENESIS OF GLU-18; GLU-127 AND HIS-130.
[10]	"Structure of a unique twofold symmetric haem-binding site." Frolow F., Kalb A.J., Yariv J. Nat. Struct. Biol. 1:453-460(1994) [PubMed: 7664064] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH HEME AND MANGANESE IONS.
[11]	"Structure of a monoclinic crystal form of cyctochrome b1 (bacterioferritin) from E. coli." Dautant A., Meyer J.-B., Yariv J., Precigoux G., Sweet R.M., Kalb A.J., Frolow F. Acta Crystallogr. D 54:16-24(1998) [PubMed: 9867433] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.94 ANGSTROMS) IN COMPLEX WITH HEME AND MANGANESE IONS, SUBUNIT.
[12]	"Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form." van Eerde A., Wolterink-van Loo S., van der Oost J., Dijkstra B.W. Acta Crystallogr. F 62:1061-1066(2006) [PubMed: 17077480] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH HEME; IRON AND ZINC IONS. Strain: B / BL21.
[13]	"Monitoring the iron status of the ferroxidase center of Escherichia coli bacterioferritin using fluorescence spectroscopy." Lawson T.L., Crow A., Lewin A., Yasmin S., Moore G.R., Le Brun N.E. Biochemistry 48:9031-9039(2009) [PubMed: 19705876] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF MUTANTS PHE-35 AND PHE-133 IN COMPLEX WITH HEME AND IRON IONS, CATALYTIC ACTIVITY, ENZYME REGULATION. Strain: K12 / JM109 / ATCC 53323.
[14]	"Structural basis for iron mineralization by bacterioferritin." Crow A., Lawson T.L., Lewin A., Moore G.R., Le Brun N.E. J. Am. Chem. Soc. 131:6808-6813(2009) [PubMed: 19391621] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF METAL-FREE APOPROTEIN AND IN COMPLEXES WITH ZN(2+); FE(2+); FE(3+) AND HEME, COFACTOR, INTERNAL SURFACE IRON-BINDING SITE, MUTAGENESIS OF HIS-46 AND ASP-50, MECHANISM OF IRON MINERALIZATION. Strain: K12 / JM109 / ATCC 53323.
[15]	"Structural and mechanistic studies of a stabilized subunit dimer variant of Escherichia coli bacterioferritin identify residues required for core formation." Wong S.G., Tom-Yew S.A., Lewin A., Le Brun N.E., Moore G.R., Murphy M.E., Mauk A.G. J. Biol. Chem. 284:18873-18881(2009) [PubMed: 19439409] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ARG-128/ARG-135 DIMER IN COMPLEX WITH HEME AND ZINC IONS.
[16]	"The binding of haem and zinc in the 1.9 A X-ray structure of Escherichia coli bacterioferritin." Willies S.C., Isupov M.N., Garman E.F., Littlechild J.A. J. Biol. Inorg. Chem. 14:201-207(2009) [PubMed: 18946693] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) IN COMPLEX WITH HEME AND ZINC IONS. Strain: B / BL21.
[17]	"Monitoring and validating active site redox states in protein crystals." Antonyuk S.V., Hough M.A. Biochim. Biophys. Acta 1814:778-784(2011) [PubMed: 21215826] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH HEME.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M27176 mRNA. Translation: AAC13987.1.
AF058450 Genomic DNA. Translation: AAC14288.1.
U18997 Genomic DNA. Translation: AAA58133.1.
U00096 Genomic DNA. Translation: AAC76361.1.
AP009048 Genomic DNA. Translation: BAE77955.1.
L28106 Genomic DNA. Translation: AAC36929.1.

PIR

FREC. JV0032.

RefSeq

NP_417795.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BCF	X-ray	2.90	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
1BFR	X-ray	2.94	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X	1-158	[»]
2HTN	X-ray	2.50	A/B/C/D/E/F/G/H	1-158	[»]
2VXI	X-ray	1.91	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
2Y3Q	X-ray	1.55	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1J	X-ray	2.70	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1L	X-ray	2.50	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1M	X-ray	2.70	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1N	X-ray	2.80	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1O	X-ray	2.95	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1P	X-ray	2.40	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E1Q	X-ray	2.60	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]
3E2C	X-ray	1.80	A/B	1-158	[»]
3GHQ	X-ray	2.70	A/B/C/D/E/F/G/H/I/J/K/L	1-158	[»]

ProteinModelPortal

P0ABD3.

SMR

P0ABD3. Positions 1-157.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36167N.

IntAct

P0ABD3. 4 interactions.

2D gel databases

ECO2DBASE

C014.3. 6TH EDITION.

Proteomic databases

PRIDE

P0ABD3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001836; EBESCP00000001836; EBESCG00000001514.
EBESCT00000017112; EBESCP00000016403; EBESCG00000016171.

GeneID

947839.

GenomeReviews

Gene locus JW3298 in contig AP009048_GR.
Gene locus b3336 in contig U00096_GR.

KEGG

ecj:JW3298.
eco:b3336.

PATRIC

32122104. VBIEscCol129921_3429.

Organism-specific databases

EchoBASE

EB0111.

EcoGene

EG10113. bfr.

Phylogenomic databases

eggNOG

COG2193.

GeneTree

EBGT00050000011195.

HOGENOM

HBG288894.

OMA

NMQVLDP.

PhylomeDB

P0ABD3.

ProtClustDB

PRK10635.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10113-MONOMER.

Gene expression databases

Genevestigator

P0ABD3.

Family and domain databases

InterPro

IPR002024. Bacterioferritin.
IPR009040. Ferritin-like.
IPR012347. Ferritin-rel.
IPR009078. Ferritin/RR-like.
IPR008331. Ferritin_DPS_dom.
[Graphical view]

Gene3D

G3DSA:1.20.1260.10. Ferritin_rel. 1 hit.

KO

K03594.

Pfam

PF00210. Ferritin. 1 hit.
[Graphical view]

PIRSF

PIRSF002560. Bacterioferritin. 1 hit.

PRINTS

PR00601. BACFERRITIN.

SUPFAM

SSF47240. Ferritin/RR_like. 1 hit.

TIGRFAMs

TIGR00754. Bfr. 1 hit.

PROSITE

PS00549. BACTERIOFERRITIN. 1 hit.
PS50905. FERRITIN_LIKE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

BFR_ECOLI

Accession

Primary (citable) accession number: P0ABD3
Secondary accession number(s): O68931, P11056, Q2M701

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 25, 2005
Last sequence update:	October 25, 2005
Last modified:	January 25, 2012
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program