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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)DescriptionActionsGraphical viewLength
Metal bindingi91Iron1
Metal bindingi133Iron1
Active sitei1341
Metal bindingi137Iron1

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
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11440. def.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL4976.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00000827792 – 169Peptide deformylaseAdd BLAST168

Proteomic databases

EPDiP0A6K3.
PaxDbiP0A6K3.
PRIDEiP0A6K3.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi4263416. 16 interactors.
DIPiDIP-47953N.
IntActiP0A6K3. 13 interactors.
STRINGi511145.b3287.

Chemistry databases

BindingDBiP0A6K3.

Structurei

Secondary structure

1169
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 15Combined sources4
Helixi26 – 41Combined sources16
Beta strandi45 – 48Combined sources4
Helixi49 – 52Combined sources4
Beta strandi56 – 61Combined sources6
Beta strandi65 – 68Combined sources4
Beta strandi71 – 82Combined sources12
Beta strandi85 – 89Combined sources5
Beta strandi92 – 94Combined sources3
Beta strandi99 – 103Combined sources5
Beta strandi105 – 112Combined sources8
Beta strandi114 – 116Combined sources3
Beta strandi118 – 123Combined sources6
Helixi125 – 138Combined sources14
Helixi143 – 146Combined sources4
Helixi149 – 165Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6K3.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
InParanoidiP0A6K3.
KOiK01462.
OMAiVCIQHEI.
PhylomeDBiP0A6K3.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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.
WP_000114984.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76312; AAC76312; b3287.
BAE78005; BAE78005; BAE78005.
GeneIDi947780.
KEGGiecj:JW3248.
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.
WP_000114984.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263416. 16 interactors.
DIPiDIP-47953N.
IntActiP0A6K3. 13 interactors.
STRINGi511145.b3287.

Chemistry databases

BindingDBiP0A6K3.
ChEMBLiCHEMBL4976.

Proteomic databases

EPDiP0A6K3.
PaxDbiP0A6K3.
PRIDEiP0A6K3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76312; AAC76312; b3287.
BAE78005; BAE78005; BAE78005.
GeneIDi947780.
KEGGiecj:JW3248.
eco:b3287.
PATRICi32122006. VBIEscCol129921_3380.

Organism-specific databases

EchoBASEiEB1410.
EcoGeneiEG11440. def.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
InParanoidiP0A6K3.
KOiK01462.
OMAiVCIQHEI.
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

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

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: November 2, 2016
This is version 109 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

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 one 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.