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Protein

Peptide deformylase

Gene

def

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

Functioni

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.

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Cofactori

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per monomer.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911Iron
Metal bindingi133 – 1331Iron
Active sitei134 – 1341
Metal bindingi137 – 1371Iron

GO - Molecular functioni

  • ferrous iron binding Source: EcoCyc
  • hydrolase activity Source: EcoliWiki
  • peptide deformylase activity Source: EcoliWiki
  • ribosome binding Source: EcoCyc
  • zinc ion binding Source: EcoliWiki

GO - Biological processi

  • co-translational protein modification Source: EcoCyc
  • N-terminal protein amino acid modification Source: EcoliWiki
  • peptidyl-methionine modification Source: GO_Central
  • translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11440-MONOMER.
ECOL316407:JW3248-MONOMER.
MetaCyc:EG11440-MONOMER.
BRENDAi3.5.1.88. 2026.
SABIO-RKP0A6K3.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Synonyms:fms
Ordered Locus Names:b3287, JW3248
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11440. def.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 169168Peptide deformylasePRO_0000082779Add
BLAST

Proteomic databases

PaxDbiP0A6K3.
PRIDEiP0A6K3.

Interactioni

Subunit structurei

Monomer.

Binary interactionsi

WithEntry#Exp.IntActNotes
rplDP607231EBI-548913,EBI-545597
usgP083901EBI-548913,EBI-548921
yaeBP286341EBI-548913,EBI-1114692

Protein-protein interaction databases

DIPiDIP-47953N.
IntActiP0A6K3. 13 interactions.
STRINGi511145.b3287.

Structurei

Secondary structure

1
169
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 154Combined sources
Helixi26 – 4116Combined sources
Beta strandi45 – 484Combined sources
Helixi49 – 524Combined sources
Beta strandi56 – 616Combined sources
Beta strandi65 – 684Combined sources
Beta strandi71 – 8212Combined sources
Beta strandi85 – 895Combined sources
Beta strandi92 – 943Combined sources
Beta strandi99 – 1035Combined sources
Beta strandi105 – 1128Combined sources
Beta strandi114 – 1163Combined sources
Beta strandi118 – 1236Combined sources
Helixi125 – 13814Combined sources
Helixi143 – 1464Combined sources
Helixi149 – 16517Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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/C2-169[»]
1G2AX-ray1.75A/B/C2-169[»]
1ICJX-ray1.90A/B/C2-169[»]
1LRUX-ray2.10A/B/C2-169[»]
1XEMX-ray1.76A2-169[»]
1XENX-ray1.85A2-169[»]
1XEOX-ray1.30A2-169[»]
2AI8X-ray1.70A/B/C2-169[»]
2DEFNMR-A3-148[»]
2DTFmodel-A1-169[»]
2KMNNMR-A2-148[»]
2W3TX-ray1.69A2-169[»]
2W3UX-ray1.96A2-169[»]
3K6LX-ray2.15A/B/C1-169[»]
4AL2X-ray2.60A/B/C2-169[»]
4AL3X-ray1.98A2-169[»]
4V5BX-ray3.74A5147-162[»]
ProteinModelPortaliP0A6K3.
SMRiP0A6K3. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6K3.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiP0A6K3.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.
PhylomeDBiP0A6K3.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P0A6K3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT
60 70 80 90 100
QVDIHQRIIV IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL
110 120 130 140 150
VPRAEKVKIR ALDRDGKPFE LEADGLLAIC IQHEMDHLVG KLFMDYLSPL
160
KQQRIRQKVE KLDRLKARA
Length:169
Mass (Da):19,328
Last modified:January 23, 2007 - v2
Checksum:iC485EB6C1D2D91B8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS23107.
RefSeqiNP_417745.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC76312; AAC76312; b3287.
BAE78005; BAE78005; BAE78005.
GeneIDi947780.
KEGGiecj:Y75_p3890.
eco:b3287.
PATRICi32122006. VBIEscCol129921_3380.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS23107.
RefSeqiNP_417745.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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/C2-169[»]
1G2AX-ray1.75A/B/C2-169[»]
1ICJX-ray1.90A/B/C2-169[»]
1LRUX-ray2.10A/B/C2-169[»]
1XEMX-ray1.76A2-169[»]
1XENX-ray1.85A2-169[»]
1XEOX-ray1.30A2-169[»]
2AI8X-ray1.70A/B/C2-169[»]
2DEFNMR-A3-148[»]
2DTFmodel-A1-169[»]
2KMNNMR-A2-148[»]
2W3TX-ray1.69A2-169[»]
2W3UX-ray1.96A2-169[»]
3K6LX-ray2.15A/B/C1-169[»]
4AL2X-ray2.60A/B/C2-169[»]
4AL3X-ray1.98A2-169[»]
4V5BX-ray3.74A5147-162[»]
ProteinModelPortaliP0A6K3.
SMRiP0A6K3. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-47953N.
IntActiP0A6K3. 13 interactions.
STRINGi511145.b3287.

Chemistry

BindingDBiP0A6K3.
ChEMBLiCHEMBL4976.

Proteomic databases

PaxDbiP0A6K3.
PRIDEiP0A6K3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76312; AAC76312; b3287.
BAE78005; BAE78005; BAE78005.
GeneIDi947780.
KEGGiecj:Y75_p3890.
eco:b3287.
PATRICi32122006. VBIEscCol129921_3380.

Organism-specific databases

EchoBASEiEB1410.
EcoGeneiEG11440. def.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiP0A6K3.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.
PhylomeDBiP0A6K3.

Enzyme and pathway databases

BioCyciEcoCyc:EG11440-MONOMER.
ECOL316407:JW3248-MONOMER.
MetaCyc:EG11440-MONOMER.
BRENDAi3.5.1.88. 2026.
SABIO-RKP0A6K3.

Miscellaneous databases

EvolutionaryTraceiP0A6K3.
PROiP0A6K3.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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.

Entry informationi

Entry nameiDEF_ECOLI
AccessioniPrimary (citable) accession number: P0A6K3
Secondary accession number(s): P27251, Q2M6V1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 99 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

External Data

Dasty 3

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 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.