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Protein

Deferrochelatase/peroxidase EfeB

Gene

efeB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact. Also displays peroxidase activity on guaiacol in vitro.2 Publications

Cofactori

heme b1 PublicationNote: Binds 1 heme b (iron(II)-protoporphyrin IX) group non-covalently per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi329 – 3291Iron (heme proximal ligand); via tele nitrogen
Binding sitei347 – 3471Heme

GO - Molecular functioni

  • heme binding Source: EcoliWiki
  • metal ion binding Source: UniProtKB-KW
  • oxidoreductase activity, acting on a heme group of donors Source: EcoCyc
  • peroxidase activity Source: EcoliWiki

GO - Biological processi

  • cellular oxidant detoxification Source: GOC
  • cellular response to DNA damage stimulus Source: EcoliWiki
  • ferrous iron transport Source: InterPro
  • iron assimilation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase, Peroxidase

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11735-MONOMER.
ECOL316407:JW1004-MONOMER.
MetaCyc:EG11735-MONOMER.

Protein family/group databases

PeroxiBasei5870. EcoDyPrx01_K12.
TCDBi2.A.108.2.3. the iron/lead transporter (ilt) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Deferrochelatase/peroxidase EfeB (EC:1.11.1.-)
Gene namesi
Name:efeB
Synonyms:ycdB
Ordered Locus Names:b1019, JW1004
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11735. efeB.

Subcellular locationi

GO - Cellular componenti

  • periplasmic space Source: EcoliWiki
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3535Tat-type signalAdd
BLAST
Chaini36 – 423388Deferrochelatase/peroxidase EfeBPRO_0000013817Add
BLAST

Post-translational modificationi

Exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven. Can also be exported by the Sec system.

Proteomic databases

EPDiP31545.
PaxDbiP31545.
PRIDEiP31545.

Expressioni

Inductioni

Repressed by Fur in the presence of iron. Repressed at high pH by the two-component regulatory system CpxA/CpxR.2 Publications

Interactioni

Subunit structurei

Homodimer. Part of a ferrous iron transporter composed of EfeU, EfeO and EfeB. However, this EfeUOB tripartite iron transporter is defective in E.coli strain K12 due to a frameshift mutation in EfeU.3 Publications

Protein-protein interaction databases

BioGridi4263253. 11 interactions.
IntActiP31545. 8 interactions.
STRINGi511145.b1019.

Structurei

Secondary structure

1
423
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi49 – 513Combined sources
Beta strandi58 – 603Combined sources
Beta strandi62 – 665Combined sources
Beta strandi70 – 7910Combined sources
Helixi84 – 10320Combined sources
Beta strandi125 – 1273Combined sources
Beta strandi133 – 1397Combined sources
Helixi140 – 1434Combined sources
Turni145 – 1484Combined sources
Helixi150 – 1523Combined sources
Helixi170 – 1723Combined sources
Beta strandi176 – 18510Combined sources
Helixi186 – 19914Combined sources
Turni201 – 2033Combined sources
Beta strandi204 – 21310Combined sources
Helixi216 – 2205Combined sources
Turni221 – 2233Combined sources
Beta strandi232 – 2365Combined sources
Helixi245 – 2517Combined sources
Helixi262 – 2643Combined sources
Beta strandi268 – 27710Combined sources
Helixi279 – 2835Combined sources
Helixi287 – 2948Combined sources
Turni298 – 3003Combined sources
Helixi315 – 3173Combined sources
Beta strandi322 – 3243Combined sources
Helixi329 – 3335Combined sources
Helixi340 – 3434Combined sources
Beta strandi350 – 3567Combined sources
Beta strandi362 – 37312Combined sources
Turni375 – 3784Combined sources
Helixi379 – 3868Combined sources
Helixi390 – 3934Combined sources
Beta strandi395 – 40511Combined sources
Helixi418 – 4225Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Y4DX-ray2.00A/B36-423[»]
2Y4EX-ray2.30A/B36-423[»]
2Y4FX-ray2.70A/B36-423[»]
ProteinModelPortaliP31545.
SMRiP31545. Positions 40-423.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31545.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni236 – 2383Heme binding
Regioni334 – 3363Heme binding

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105DBE. Bacteria.
COG2837. LUCA.
HOGENOMiHOG000236941.
InParanoidiP31545.
KOiK16301.
OMAiVERWDRT.
OrthoDBiEOG6F55G9.
PhylomeDBiP31545.

Family and domain databases

InterProiIPR011008. Dimeric_a/b-barrel.
IPR006314. Dyp_peroxidase.
IPR006313. EfeB.
IPR006311. TAT_signal.
[Graphical view]
PfamiPF04261. Dyp_perox. 1 hit.
[Graphical view]
SUPFAMiSSF54909. SSF54909. 1 hit.
TIGRFAMsiTIGR01413. Dyp_perox_fam. 1 hit.
TIGR01412. tat_substr_1. 1 hit.
PROSITEiPS51404. DYP_PEROXIDASE. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P31545-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQYKDENGVN EPSRRRLLKV IGALALAGSC PVAHAQKTQS APGTLSPDAR
60 70 80 90 100
NEKQPFYGEH QAGILTPQQA AMMLVAFDVL ASDKADLERL FRLLTQRFAF
110 120 130 140 150
LTQGGAAPET PNPRLPPLDS GILGGYIAPD NLTITLSVGH SLFDERFGLA
160 170 180 190 200
PQMPKKLQKM TRFPNDSLDA ALCHGDVLLQ ICANTQDTVI HALRDIIKHT
210 220 230 240 250
PDLLSVRWKR EGFISDHAAR SKGKETPINL LGFKDGTANP DSQNDKLMQK
260 270 280 290 300
VVWVTADQQE PAWTIGGSYQ AVRLIQFRVE FWDRTPLKEQ QTIFGRDKQT
310 320 330 340 350
GAPLGMQHEH DVPDYASDPE GKVIALDSHI RLANPRTAES ESSLMLRRGY
360 370 380 390 400
SYSLGVTNSG QLDMGLLFVC YQHDLEKGFL TVQKRLNGEA LEEYVKPIGG
410 420
GYFFALPGVK DANDYFGSAL LRV
Length:423
Mass (Da):46,754
Last modified:November 1, 1997 - v2
Checksum:i65D381F829DB2570
GO

Mass spectrometryi

Molecular mass is 43814 Da from positions 36 - 423. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74104.1.
AP009048 Genomic DNA. Translation: BAA35800.1.
D10391 Genomic DNA. Translation: BAA01229.1.
PIRiA64844.
RefSeqiNP_415538.1. NC_000913.3.
WP_001199471.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74104; AAC74104; b1019.
BAA35800; BAA35800; BAA35800.
GeneIDi946500.
KEGGiecj:JW1004.
eco:b1019.
PATRICi32117271. VBIEscCol129921_1059.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74104.1.
AP009048 Genomic DNA. Translation: BAA35800.1.
D10391 Genomic DNA. Translation: BAA01229.1.
PIRiA64844.
RefSeqiNP_415538.1. NC_000913.3.
WP_001199471.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Y4DX-ray2.00A/B36-423[»]
2Y4EX-ray2.30A/B36-423[»]
2Y4FX-ray2.70A/B36-423[»]
ProteinModelPortaliP31545.
SMRiP31545. Positions 40-423.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263253. 11 interactions.
IntActiP31545. 8 interactions.
STRINGi511145.b1019.

Protein family/group databases

PeroxiBasei5870. EcoDyPrx01_K12.
TCDBi2.A.108.2.3. the iron/lead transporter (ilt) family.

Proteomic databases

EPDiP31545.
PaxDbiP31545.
PRIDEiP31545.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74104; AAC74104; b1019.
BAA35800; BAA35800; BAA35800.
GeneIDi946500.
KEGGiecj:JW1004.
eco:b1019.
PATRICi32117271. VBIEscCol129921_1059.

Organism-specific databases

EchoBASEiEB1686.
EcoGeneiEG11735. efeB.

Phylogenomic databases

eggNOGiENOG4105DBE. Bacteria.
COG2837. LUCA.
HOGENOMiHOG000236941.
InParanoidiP31545.
KOiK16301.
OMAiVERWDRT.
OrthoDBiEOG6F55G9.
PhylomeDBiP31545.

Enzyme and pathway databases

BioCyciEcoCyc:EG11735-MONOMER.
ECOL316407:JW1004-MONOMER.
MetaCyc:EG11735-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP31545.
PROiP31545.

Family and domain databases

InterProiIPR011008. Dimeric_a/b-barrel.
IPR006314. Dyp_peroxidase.
IPR006313. EfeB.
IPR006311. TAT_signal.
[Graphical view]
PfamiPF04261. Dyp_perox. 1 hit.
[Graphical view]
SUPFAMiSSF54909. SSF54909. 1 hit.
TIGRFAMsiTIGR01413. Dyp_perox_fam. 1 hit.
TIGR01412. tat_substr_1. 1 hit.
PROSITEiPS51404. DYP_PEROXIDASE. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli."
    Kim S.-K., Makino K., Amemura M., Shinagawa H., Nakata A.
    J. Bacteriol. 175:1316-1324(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 196-423.
    Strain: K12.
  5. "Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis."
    McHugh J.P., Rodriguez-Quinones F., Abdul-Tehrani H., Svistunenko D.A., Poole R.K., Cooper C.E., Andrews S.C.
    J. Biol. Chem. 278:29478-29486(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  6. "YcdB from Escherichia coli reveals a novel class of Tat-dependently translocated hemoproteins."
    Sturm A., Schierhorn A., Lindenstrauss U., Lilie H., Brueser T.
    J. Biol. Chem. 281:13972-13978(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A PEROXIDASE, SUBUNIT, EXPORT VIA THE TAT-SYSTEM, SUBCELLULAR LOCATION, COFACTOR, MASS SPECTROMETRY.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  7. "Export pathway selectivity of Escherichia coli twin arginine translocation signal peptides."
    Tullman-Ercek D., DeLisa M.P., Kawarasaki Y., Iranpour P., Ribnicky B., Palmer T., Georgiou G.
    J. Biol. Chem. 282:8309-8316(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: EXPORT VIA THE TAT-SYSTEM AND THE SEC-SYSTEM.
  8. "EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7."
    Cao J., Woodhall M.R., Alvarez J., Cartron M.L., Andrews S.C.
    Mol. Microbiol. 65:857-875(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION, SUBUNIT, LACK OF ACTIVITY IN STRAIN K12.
    Strain: K12.
  9. "Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact."
    Letoffe S., Heuck G., Delepelaire P., Lange N., Wandersman C.
    Proc. Natl. Acad. Sci. U.S.A. 106:11719-11724(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DEFERROCHELATASE.
    Strain: K12 / MG1655 / ATCC 47076.
  10. "Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-secreted periplasmic protein with a potential role in iron transport."
    Cartron M.L., Mitchell S.A., Woodhall M.R., Andrews S.C., Watson K.A.
    Acta Crystallogr. F 63:37-41(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION.
    Strain: K12.
  11. "EfeB, the peroxidase component of the EfeUOB bacterial Fe(II) transport system, also shows novel removal of iron from heme."
    Bamford V.A., Andrews S.C., Watson K.A.
    Submitted (JAN-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 36-423 OF APOPROTEIN AND IN COMPLEXES WITH PROTOPORPHYRIN IX AND HEME, SUBUNIT.
    Strain: K12.

Entry informationi

Entry nameiEFEB_ECOLI
AccessioniPrimary (citable) accession number: P31545
Secondary accession number(s): P75903
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: November 1, 1997
Last modified: March 16, 2016
This is version 126 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.