efeB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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Standard name

YcdB

Synonyms

conserved protein[1], B1019[2][1], YcdB[2][1] , ECK1009, JW1004, ycdB, b1019

Product description

conserved protein[2]; heme-containing peroxidase[3]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki. See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0004601

peroxidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0575

F

Seeded from EcoCyc (v14.0)

complete

GO:0005506

iron ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006313

F

Seeded from EcoCyc (v14.0)

complete

GO:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc (v14.0)

complete

GO:0016684

oxidoreductase activity, acting on peroxide as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006313

F

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0574

C

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0200

C

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006313

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071[4]

IEP: Inferred from Expression Pattern

P

complete

GO:0020037

heme binding

PMID:16551627[5]

IDA: Inferred from Direct Assay

F

Figure 3b. Mass spectrometry indicates heme is bound noncovalently.

complete

GO:0004601

peroxidase activity

PMID:16551627[5]

IDA: Inferred from Direct Assay

F

Figure 5. Peroxidase activity highest at pH 4.0.

complete

GO:0042597

periplasmic space

PMID:16551627[5]

IDA: Inferred from Direct Assay

C

Fig. 1

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

dnaK

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

fdhF

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

uspG

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

rplB

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

uxaA

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

phoB

PMID:16606699[6]

Experiment(s):EBI-1138657

Protein

dinG

PMID:16606699[6]

Experiment(s):EBI-1138657
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Notes

Localization

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Compartment Description Evidence Reference/Source Notes

periplasm


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

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
Length

423

Mol. Wt

46.755 kDa

pI

6.9 (calculated)

Extinction coefficient

38,390 - 38,890 (calc based on 11 Y, 4 W, and 4 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

motif

1-35

UniProt Manual:Signal Peptides

UniProt:P31545

Domain

61..411

PF04261 Dyp-type peroxidase family

PMID:19920124[7]

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<motif_map/>

Structure
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Structures

<beststructure> gene=efeB taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128983

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946500

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003451

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P31545

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11735

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11735

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946500

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001674

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1686

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
  5. ↑ 5.0 5.1 5.2 Sturm, A et al. (2006) YcdB from Escherichia coli reveals a novel class of Tat-dependently translocated hemoproteins. J. Biol. Chem. 281 13972-8 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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