def:Gene Product(s)

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

Nomenclature

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

Standard name

Def

Synonyms

peptide deformylase[1], B3287[2][1], Fms[2][1], Def[2][1] , ECK3273, fms, JW3248, b3287

Product description

peptide deformylase[2][3]

Peptide deformylase; N-formylmethionylaminoacyl-tRNA deformylase[4]

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.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0006412

translation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00163

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000181

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0648

P

Seeded from EcoCyc (v14.0)

complete

GO:0042586

peptide deformylase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00163

F

Seeded from EcoCyc (v14.0)

complete

GO:0042586

peptide deformylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000181

F

Seeded from EcoCyc (v14.0)

complete

GO:0042586

peptide deformylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.1.88

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:11985624[5]

IDA: Inferred from Direct Assay

F

complete

GO:0008270

zinc ion binding

PMID:8244948[6]

IDA: Inferred from Direct Assay

F

complete

GO:0042586

peptide deformylase activity

PMID:7896716[7]

IDA: Inferred from Direct Assay

F

complete

GO:0008270

zinc ion binding

PMID:7896716[7]

IDA: Inferred from Direct Assay

F

complete

GO:0016787

hydrolase activity

PMID:7896716[7]

IDA: Inferred from Direct Assay

F

complete

GO:0031365

N-terminal protein amino acid modification

PMID:7896716[7]

IDA: Inferred from Direct Assay

P

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

rplD

PMID:15690043[8]

Experiment(s):EBI-880244

Protein

usg

PMID:15690043[8]

Experiment(s):EBI-883708

Protein

yaeB

PMID:16606699[9]

Experiment(s):EBI-1145366

Protein

usg

PMID:19402753[10]

LCMS(ID Probability):99.0

Small Molecule

1,10 phenanthroline

inhibitor

PMID:7896716[7]

kinetic assay

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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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 

MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV
IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE
LEADGLLAIC IQHEMDHLVG KLFMDYLSPL KQQRIRQKVE KLDRLKARA
Length

169

Mol. Wt

19.328 kDa

pI

5.2 (calculated)

Extinction coefficient

2,980 - 3,230 (calc based on 2 Y, 0 W, and 2 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

Initiator Methionine

1

Removed

UniProt:P0A6K3

Domain

3..153

PF01327 Polypeptide deformylase

PMID:19920124[11]

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

Structures

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

Models

View models at:

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Structure figures

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Notes

  • Biochemical characterization of Fms is described in [6] and [7]

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:16131166

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947780

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010779

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6K3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11440

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11440

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947780

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001404

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1410

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 1.3 1.4 1.5 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 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. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Katayama, A et al. (2002) Systematic search for zinc-binding proteins in Escherichia coli. Eur. J. Biochem. 269 2403-13 PubMed
  6. ↑ 6.0 6.1 Meinnel, T & Blanquet, S (1993) Evidence that peptide deformylase and methionyl-tRNA(fMet) formyltransferase are encoded within the same operon in Escherichia coli. J. Bacteriol. 175 7737-40 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Meinnel, T & Blanquet, S (1995) Enzymatic properties of Escherichia coli peptide deformylase. J. Bacteriol. 177 1883-7 PubMed
  8. ↑ 8.0 8.1 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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