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Protein

Peptide deformylase

Gene

def

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

Functioni

Removes the formyl group from the N-terminal Met of newly synthesized proteins (PubMed:7896716). 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.1 Publication2 Publications

Catalytic activityi

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

Cofactori

Fe2+1 Publication, Zn2+1 Publication1 PublicationNote: Upon overproduction is isolated with 1 Fe2+ ion per monomer, a Ni2+-bound form is as active while a Zn2+-bound form is inactive (PubMed:9610360).1 Publication

Enzyme regulationi

Inhibited by 1,10-phenanthroline.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
  • peptidyl-methionine modification Source: GO_Central
  • translation Source: UniProtKB-KW

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11440-MONOMER
MetaCyc:EG11440-MONOMER
BRENDAi3.5.1.88 2026
SABIO-RKiP0A6K3

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:fms1 Publication
Ordered Locus Names:b3287, JW3248
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi

Organism-specific databases

EcoGeneiEG11440 def

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL4976
DrugBankiDB02276 (S)-2-(Phosphonoxy)Caproyl-L-Leucyl-P-Nitroanilide
DB04310 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide
DB08523 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL
DB04368 Bb-3497
DB01942 Formic Acid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000827792 – 169Peptide deformylaseAdd BLAST168

Proteomic databases

EPDiP0A6K3
PaxDbiP0A6K3
PRIDEiP0A6K3

Interactioni

Subunit structurei

Monomer.

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4263416, 59 interactors
DIPiDIP-47953N
IntActiP0A6K3, 15 interactors
STRINGi316385.ECDH10B_3461

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[»]
4AZ4X-ray1.80A2-169[»]
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
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
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

Mass spectrometryi

Molecular mass is 19175±50 Da from positions 2 - 169. Determined by MALDI. 1 Publication

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
PATRICifig|1411691.4.peg.3445

Entry informationi

Entry nameiDEF_ECOLI
AccessioniPrimary (citable) accession number: P0A6K3
Secondary accession number(s): P27251, Q2M6V1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 119 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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

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