EFEB_ECOLI
ID EFEB_ECOLI Reviewed; 423 AA.
AC P31545; P75903;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Deferrochelatase {ECO:0000305|PubMed:19564607};
DE EC=4.99.1.1 {ECO:0000269|PubMed:19564607};
DE AltName: Full=Peroxidase EfeB {ECO:0000305|PubMed:16551627};
DE EC=1.11.1.- {ECO:0000269|PubMed:16551627};
DE Flags: Precursor;
GN Name=efeB; Synonyms=ycdB; OrderedLocusNames=b1019, JW1004;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 196-423.
RC STRAIN=K12;
RX PubMed=8444794; DOI=10.1128/jb.175.5.1316-1324.1993;
RA Kim S.-K., Makino K., Amemura M., Shinagawa H., Nakata A.;
RT "Molecular analysis of the phoH gene, belonging to the phosphate regulon in
RT Escherichia coli.";
RL J. Bacteriol. 175:1316-1324(1993).
RN [5]
RP INDUCTION.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=12746439; DOI=10.1074/jbc.m303381200;
RA McHugh J.P., Rodriguez-Quinones F., Abdul-Tehrani H., Svistunenko D.A.,
RA Poole R.K., Cooper C.E., Andrews S.C.;
RT "Global iron-dependent gene regulation in Escherichia coli. A new mechanism
RT for iron homeostasis.";
RL J. Biol. Chem. 278:29478-29486(2003).
RN [6]
RP FUNCTION AS A PEROXIDASE, SUBUNIT, EXPORT VIA THE TAT-SYSTEM, SUBCELLULAR
RP LOCATION, COFACTOR, AND MASS SPECTROMETRY.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=16551627; DOI=10.1074/jbc.m511891200;
RA Sturm A., Schierhorn A., Lindenstrauss U., Lilie H., Brueser T.;
RT "YcdB from Escherichia coli reveals a novel class of Tat-dependently
RT translocated hemoproteins.";
RL J. Biol. Chem. 281:13972-13978(2006).
RN [7]
RP EXPORT VIA THE TAT-SYSTEM AND THE SEC-SYSTEM.
RX PubMed=17218314; DOI=10.1074/jbc.m610507200;
RA Tullman-Ercek D., DeLisa M.P., Kawarasaki Y., Iranpour P., Ribnicky B.,
RA Palmer T., Georgiou G.;
RT "Export pathway selectivity of Escherichia coli twin arginine translocation
RT signal peptides.";
RL J. Biol. Chem. 282:8309-8316(2007).
RN [8]
RP INDUCTION, SUBUNIT, AND LACK OF ACTIVITY IN STRAIN K12.
RC STRAIN=K12;
RX PubMed=17627767; DOI=10.1111/j.1365-2958.2007.05802.x;
RA Cao J., Woodhall M.R., Alvarez J., Cartron M.L., Andrews S.C.;
RT "EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH
RT Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in
RT E. coli O157:H7.";
RL Mol. Microbiol. 65:857-875(2007).
RN [9]
RP FUNCTION AS A DEFERROCHELATASE, AND CATALYTIC ACTIVITY.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=19564607; DOI=10.1073/pnas.0903842106;
RA Letoffe S., Heuck G., Delepelaire P., Lange N., Wandersman C.;
RT "Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:11719-11724(2009).
RN [10]
RP CRYSTALLIZATION.
RC STRAIN=K12;
RX PubMed=17183171; DOI=10.1107/s174430910604509x;
RA Cartron M.L., Mitchell S.A., Woodhall M.R., Andrews S.C., Watson K.A.;
RT "Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a
RT novel haem-containing and Tat-secreted periplasmic protein with a potential
RT role in iron transport.";
RL Acta Crystallogr. F 63:37-41(2007).
RN [11] {ECO:0007744|PDB:2Y4D, ECO:0007744|PDB:2Y4E, ECO:0007744|PDB:2Y4F}
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 36-423 OF APOPROTEIN AND IN
RP COMPLEXES WITH PROTOPORPHYRIN IX AND HEME, AND SUBUNIT.
RC STRAIN=K12;
RA Bamford V.A., Andrews S.C., Watson K.A.;
RT "EfeB, the peroxidase component of the EfeUOB bacterial Fe(II) transport
RT system, also shows novel removal of iron from heme.";
RL Submitted (JAN-2011) to the PDB data bank.
CC -!- FUNCTION: Involved in the recovery of exogenous heme iron. Extracts
CC iron from heme while preserving the protoporphyrin ring intact. Also
CC displays peroxidase activity on guaiacol in vitro.
CC {ECO:0000269|PubMed:16551627, ECO:0000269|PubMed:19564607}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 H(+) + heme b = Fe(2+) + protoporphyrin IX;
CC Xref=Rhea:RHEA:22584, ChEBI:CHEBI:15378, ChEBI:CHEBI:29033,
CC ChEBI:CHEBI:57306, ChEBI:CHEBI:60344; EC=4.99.1.1;
CC Evidence={ECO:0000269|PubMed:19564607};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:22585;
CC Evidence={ECO:0000269|PubMed:19564607};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:16551627};
CC Note=Binds 1 heme b (iron(II)-protoporphyrin IX) group non-covalently
CC per subunit. {ECO:0000269|PubMed:16551627};
CC -!- SUBUNIT: Homodimer. Part of a ferrous iron transporter composed of
CC EfeU, EfeO and EfeB. However, this EfeUOB tripartite iron transporter
CC is defective in E.coli strain K12 due to a frameshift mutation in EfeU.
CC {ECO:0000269|PubMed:16551627, ECO:0000269|PubMed:17627767,
CC ECO:0000269|Ref.11}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:16551627}.
CC -!- INDUCTION: Repressed by Fur in the presence of iron. Repressed at high
CC pH by the two-component regulatory system CpxA/CpxR.
CC {ECO:0000269|PubMed:12746439, ECO:0000269|PubMed:17627767}.
CC -!- PTM: Exported by the Tat system. The position of the signal peptide
CC cleavage has been experimentally proven. Can also be exported by the
CC Sec system.
CC -!- MASS SPECTROMETRY: Mass=43814; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:16551627};
CC -!- SIMILARITY: Belongs to the DyP-type peroxidase family. EfeB subfamily.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC74104.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35800.1; -; Genomic_DNA.
DR EMBL; D10391; BAA01229.1; -; Genomic_DNA.
DR PIR; A64844; A64844.
DR RefSeq; NP_415538.1; NC_000913.3.
DR RefSeq; WP_001199471.1; NZ_SSZK01000002.1.
DR PDB; 2Y4D; X-ray; 2.00 A; A/B=36-423.
DR PDB; 2Y4E; X-ray; 2.30 A; A/B=36-423.
DR PDB; 2Y4F; X-ray; 2.70 A; A/B=36-423.
DR PDBsum; 2Y4D; -.
DR PDBsum; 2Y4E; -.
DR PDBsum; 2Y4F; -.
DR AlphaFoldDB; P31545; -.
DR SMR; P31545; -.
DR BioGRID; 4263253; 25.
DR IntAct; P31545; 8.
DR STRING; 511145.b1019; -.
DR PeroxiBase; 5870; EcoDyPrx01_K12.
DR TCDB; 2.A.108.2.3; the iron/lead transporter (ilt) family.
DR PaxDb; P31545; -.
DR PRIDE; P31545; -.
DR EnsemblBacteria; AAC74104; AAC74104; b1019.
DR EnsemblBacteria; BAA35800; BAA35800; BAA35800.
DR GeneID; 946500; -.
DR KEGG; ecj:JW1004; -.
DR KEGG; eco:b1019; -.
DR PATRIC; fig|1411691.4.peg.1250; -.
DR EchoBASE; EB1686; -.
DR eggNOG; COG2837; Bacteria.
DR HOGENOM; CLU_039488_0_0_6; -.
DR InParanoid; P31545; -.
DR OMA; QACANDP; -.
DR PhylomeDB; P31545; -.
DR BioCyc; EcoCyc:EG11735-MON; -.
DR BioCyc; MetaCyc:EG11735-MON; -.
DR EvolutionaryTrace; P31545; -.
DR PRO; PR:P31545; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IDA:EcoCyc.
DR GO; GO:0042597; C:periplasmic space; IDA:EcoliWiki.
DR GO; GO:0004325; F:ferrochelatase activity; IEA:RHEA.
DR GO; GO:0020037; F:heme binding; IDA:EcoliWiki.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004601; F:peroxidase activity; IDA:EcoliWiki.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0033212; P:iron import into cell; IEA:InterPro.
DR InterPro; IPR011008; Dimeric_a/b-barrel.
DR InterPro; IPR006314; Dyp_peroxidase.
DR InterPro; IPR006313; EfeB.
DR InterPro; IPR006311; TAT_signal.
DR Pfam; PF04261; Dyp_perox; 1.
DR SUPFAM; SSF54909; SSF54909; 1.
DR TIGRFAMs; TIGR01413; Dyp_perox_fam; 1.
DR TIGRFAMs; TIGR01412; tat_substr_1; 1.
DR PROSITE; PS51404; DYP_PEROXIDASE; 1.
DR PROSITE; PS51318; TAT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Heme; Iron; Lyase; Metal-binding; Oxidoreductase; Periplasm;
KW Peroxidase; Reference proteome; Signal.
FT SIGNAL 1..35
FT /note="Tat-type signal"
FT CHAIN 36..423
FT /note="Deferrochelatase"
FT /id="PRO_0000013817"
FT BINDING 236..238
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000269|Ref.11, ECO:0007744|PDB:2Y4F"
FT BINDING 236..238
FT /ligand="protoporphyrin IX"
FT /ligand_id="ChEBI:CHEBI:57306"
FT /evidence="ECO:0000269|Ref.11, ECO:0007744|PDB:2Y4E"
FT BINDING 296
FT /ligand="protoporphyrin IX"
FT /ligand_id="ChEBI:CHEBI:57306"
FT /evidence="ECO:0000269|Ref.11, ECO:0007744|PDB:2Y4E"
FT BINDING 329
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="proximal binding residue"
FT /evidence="ECO:0000269|Ref.11, ECO:0007744|PDB:2Y4F"
FT BINDING 334..336
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000269|Ref.11, ECO:0007744|PDB:2Y4F"
FT BINDING 347
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000269|Ref.11, ECO:0007744|PDB:2Y4F"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 62..66
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 70..79
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 84..103
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 133..139
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:2Y4D"
FT TURN 145..148
FT /evidence="ECO:0007829|PDB:2Y4E"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 176..185
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 186..199
FT /evidence="ECO:0007829|PDB:2Y4D"
FT TURN 201..203
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 204..213
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 216..220
FT /evidence="ECO:0007829|PDB:2Y4D"
FT TURN 221..223
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 232..236
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 245..251
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 268..277
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 279..283
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 287..294
FT /evidence="ECO:0007829|PDB:2Y4D"
FT TURN 298..300
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 315..317
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 329..333
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 340..343
FT /evidence="ECO:0007829|PDB:2Y4F"
FT STRAND 350..356
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 362..373
FT /evidence="ECO:0007829|PDB:2Y4D"
FT TURN 375..378
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 379..386
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 390..393
FT /evidence="ECO:0007829|PDB:2Y4D"
FT STRAND 395..405
FT /evidence="ECO:0007829|PDB:2Y4D"
FT HELIX 418..422
FT /evidence="ECO:0007829|PDB:2Y4D"
SQ SEQUENCE 423 AA; 46754 MW; 65D381F829DB2570 CRC64;
MQYKDENGVN EPSRRRLLKV IGALALAGSC PVAHAQKTQS APGTLSPDAR NEKQPFYGEH
QAGILTPQQA AMMLVAFDVL ASDKADLERL FRLLTQRFAF LTQGGAAPET PNPRLPPLDS
GILGGYIAPD NLTITLSVGH SLFDERFGLA PQMPKKLQKM TRFPNDSLDA ALCHGDVLLQ
ICANTQDTVI HALRDIIKHT PDLLSVRWKR EGFISDHAAR SKGKETPINL LGFKDGTANP
DSQNDKLMQK VVWVTADQQE PAWTIGGSYQ AVRLIQFRVE FWDRTPLKEQ QTIFGRDKQT
GAPLGMQHEH DVPDYASDPE GKVIALDSHI RLANPRTAES ESSLMLRRGY SYSLGVTNSG
QLDMGLLFVC YQHDLEKGFL TVQKRLNGEA LEEYVKPIGG GYFFALPGVK DANDYFGSAL
LRV
