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Protein

Peptide deformylase

Gene

def

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Reviewed-Annotation score: Annotation score: 2 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.UniRule annotation

Catalytic activityi

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

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi114IronUniRule annotation1
Metal bindingi157IronUniRule annotation1
Active sitei158UniRule annotation1
Metal bindingi161IronUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:EF_3066
OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)
Taxonomic identifieri226185 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
Proteomesi
  • UP000001415 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000827821 – 187Peptide deformylaseAdd BLAST187

Interactioni

Protein-protein interaction databases

STRINGi226185.EF3066.

Structurei

Secondary structure

1187
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 6Combined sources3
Helixi13 – 16Combined sources4
Helixi28 – 45Combined sources18
Helixi47 – 53Combined sources7
Beta strandi59 – 62Combined sources4
Helixi63 – 66Combined sources4
Beta strandi70 – 77Combined sources8
Beta strandi89 – 101Combined sources13
Beta strandi105 – 108Combined sources4
Beta strandi127 – 136Combined sources10
Beta strandi142 – 148Combined sources7
Helixi149 – 162Combined sources14
Helixi167 – 170Combined sources4
Beta strandi173 – 175Combined sources3
Beta strandi184 – 186Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OS0X-ray1.30A1-187[»]
2OS1X-ray1.50A1-187[»]
ProteinModelPortaliQ82ZJ0.
SMRiQ82ZJ0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ82ZJ0.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107YB9. Bacteria.
COG0242. LUCA.
KOiK01462.
OMAiMILMKDI.

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.

Q82ZJ0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITMKDIIRE GNPTLRAVAE EVPVPITEED RQLGEDMLTF LKNSQDPVKA
60 70 80 90 100
EELQLRGGVG LAAPQLDISK RIIAVHVPSN DPENETPSLS TVMYNPKILS
110 120 130 140 150
HSVQDVCLGE GEGCLSVDRD VPGYVVRHNK ITVSYFDMAG EKHKVRLKNY
160 170 180
EAIVVQHEID HINGIMFYDH INKENPFALK EGVLVIE
Length:187
Mass (Da):20,912
Last modified:June 1, 2003 - v1
Checksum:i9CAF46335311B0B2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016830 Genomic DNA. Translation: AAO82748.1.
RefSeqiNP_816678.1. NC_004668.1.
WP_002354981.1. NZ_KE136524.1.

Genome annotation databases

EnsemblBacteriaiAAO82748; AAO82748; EF_3066.
GeneIDi1201912.
KEGGiefa:EF3066.
PATRICi21856293. VBIEntFae7065_2859.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016830 Genomic DNA. Translation: AAO82748.1.
RefSeqiNP_816678.1. NC_004668.1.
WP_002354981.1. NZ_KE136524.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OS0X-ray1.30A1-187[»]
2OS1X-ray1.50A1-187[»]
ProteinModelPortaliQ82ZJ0.
SMRiQ82ZJ0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi226185.EF3066.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO82748; AAO82748; EF_3066.
GeneIDi1201912.
KEGGiefa:EF3066.
PATRICi21856293. VBIEntFae7065_2859.

Phylogenomic databases

eggNOGiENOG4107YB9. Bacteria.
COG0242. LUCA.
KOiK01462.
OMAiMILMKDI.

Miscellaneous databases

EvolutionaryTraceiQ82ZJ0.

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_ENTFA
AccessioniPrimary (citable) accession number: Q82ZJ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: November 2, 2016
This is version 84 of the entry and version 1 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.