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P0A6K3 (DEF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 86. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptide deformylase

Short name=PDF
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:def
Synonyms:fms
Ordered Locus Names:b3287, JW3248
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length169 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. HAMAP-Rule MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163

Cofactor

Binds 1 Fe2+ ion per monomer. Ref.7

Subunit structure

Monomer.

Sequence similarities

Belongs to the polypeptide deformylase family.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed HAMAP-Rule MF_00163
Chain2 – 169168Peptide deformylase HAMAP-Rule MF_00163
PRO_0000082779

Sites

Active site1341
Metal binding911Iron
Metal binding1331Iron
Metal binding1371Iron

Secondary structure

................................ 169
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A6K3 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: C485EB6C1D2D91B8

FASTA16919,328
        10         20         30         40         50         60 
MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV 

        70         80         90        100        110        120 
IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE 

       130        140        150        160 
LEADGLLAIC IQHEMDHLVG KLFMDYLSPL KQQRIRQKVE KLDRLKARA 

« Hide

References

« Hide 'large scale' references
[1]"Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation."
Mazel D., Pochet S., Marliere P.
EMBO J. 13:914-923(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
Strain: K12.
[2]"Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli."
Guillon J.-M., Mechulam Y., Schmitter J.-M., Blanquet S., Fayat G.
J. Bacteriol. 174:4294-4301(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12 / K37.
[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 277:1453-1462(1997) [PubMed] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control."
Meinnel T., Guillon J.-M., Mechulam Y., Blanquet S.
J. Bacteriol. 175:993-1000(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16.
Strain: K12 / K37.
[6]"Enzymatic properties of Escherichia coli peptide deformylase."
Meinnel T., Blanquet S.
J. Bacteriol. 177:1883-1887(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[7]"Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site."
Groche D., Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.
Biochem. Biophys. Res. Commun. 246:342-346(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: COFACTOR.
[8]"A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase."
Meinnel T., Blanquet S., Dardel F.
J. Mol. Biol. 262:375-386(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR.
[9]"Solution structure of nickel-peptide deformylase."
Dardel F., Ragusa S., Lazennec C., Blanquet S., Meinnel T.
J. Mol. Biol. 280:501-513(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR.
[10]"Crystal structure of the Escherichia coli peptide deformylase."
Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D.
Biochemistry 36:13904-13909(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
[11]Erratum
Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D.
Biochemistry 37:13042-13042(1998)
[12]"Structure of peptide deformylase and identification of the substrate binding site."
Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.
J. Biol. Chem. 273:11413-11416(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[13]"Iron center, substrate recognition and mechanism of peptide deformylase."
Becker A., Schlichting I., Kabsch W., Groche D., Schultz S., Wagner A.F.
Nat. Struct. Biol. 5:1053-1058(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[14]"Structural basis for the design of antibiotics targeting peptide deformylase."
Hao B., Gong W., Rajagopalan P.T.R., Zhou Y., Pei D., Chan M.K.
Biochemistry 38:4712-4719(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X77800 Genomic DNA. Translation: CAA54826.1.
X63666 Genomic DNA. Translation: CAA45206.1.
X65946 Genomic DNA. No translation available.
X77091 Genomic DNA. Translation: CAA54367.1.
U18997 Genomic DNA. Translation: AAA58084.1.
U00096 Genomic DNA. Translation: AAC76312.1.
AP009048 Genomic DNA. Translation: BAE78005.1.
PIRS23107.
RefSeqNP_417745.1. NC_000913.3.
YP_492146.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BS4X-ray1.90A/B/C2-169[»]
1BS5X-ray2.50A/B/C2-169[»]
1BS6X-ray2.10A/B/C2-169[»]
1BS7X-ray2.50A/B/C2-169[»]
1BS8X-ray2.20A/B/C2-169[»]
1BSJX-ray3.00A2-169[»]
1BSKX-ray3.00A2-169[»]
1BSZX-ray1.90A/B/C2-169[»]
1DEFNMR-A2-148[»]
1DFFX-ray2.88A2-165[»]
1DTFmodel-A1-169[»]
1G27X-ray2.10A/B/C2-168[»]
1G2AX-ray1.75A/B/C2-168[»]
1ICJX-ray1.90A/B/C2-169[»]
1LRUX-ray2.10A/B/C2-168[»]
1XEMX-ray1.76A2-169[»]
1XENX-ray1.85A2-169[»]
1XEOX-ray1.30A2-169[»]
2AI8X-ray1.70A/B/C2-168[»]
2DEFNMR-A3-148[»]
2DTFmodel-A1-169[»]
2KMNNMR-A2-148[»]
2VHMX-ray3.745148-162[»]
2W3TX-ray1.69A2-169[»]
2W3UX-ray1.96A2-169[»]
3K6LX-ray2.15A/B/C1-169[»]
4AL2X-ray2.60A/B/C2-169[»]
4AL3X-ray1.98A2-169[»]
ProteinModelPortalP0A6K3.
SMRP0A6K3. Positions 2-168.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-47953N.
IntActP0A6K3. 13 interactions.
STRING511145.b3287.

Chemistry

BindingDBP0A6K3.
ChEMBLCHEMBL4976.

Proteomic databases

PaxDbP0A6K3.
PRIDEP0A6K3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76312; AAC76312; b3287.
BAE78005; BAE78005; BAE78005.
GeneID12934422.
947780.
KEGGecj:Y75_p3890.
eco:b3287.
PATRIC32122006. VBIEscCol129921_3380.

Organism-specific databases

EchoBASEEB1410.
EcoGeneEG11440. def.

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAMAETMYE.
OrthoDBEOG664CMF.
PhylomeDBP0A6K3.
ProtClustDBPRK00150.

Enzyme and pathway databases

BioCycEcoCyc:EG11440-MONOMER.
ECOL316407:JW3248-MONOMER.
MetaCyc:EG11440-MONOMER.
SABIO-RKP0A6K3.

Gene expression databases

GenevestigatorP0A6K3.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0A6K3.
PROP0A6K3.

Entry information

Entry nameDEF_ECOLI
AccessionPrimary (citable) accession number: P0A6K3
Secondary accession number(s): P27251, Q2M6V1
Entry history
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 86 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene