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Protein

Peptide deformylase

Gene

def

Organism
Treponema pallidum (strain Nichols)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi86 – 861IronBy similarity
Metal bindingi128 – 1281IronBy similarity
Active sitei129 – 1291By similarity
Metal bindingi132 – 1321IronBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciTPAL243276:GC1H-803-MONOMER.

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
Ordered Locus Names:TP_0757
OrganismiTreponema pallidum (strain Nichols)
Taxonomic identifieri243276 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesSpirochaetaceaeTreponema
ProteomesiUP000000811 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 162162Peptide deformylasePRO_0000082869Add
BLAST

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
TP_0961O839272EBI-1199001,EBI-1198947

Protein-protein interaction databases

IntActiO83738. 40 interactions.
MINTiMINT-6481412.
STRINGi243276.TP0757.

Structurei

3D structure databases

ProteinModelPortaliO83738.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiIRSAEWY.
OrthoDBiEOG664CMF.

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.

O83738-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELKFLGEPC LTTVSEPVSE VDEQLRAFIS GMFRVMRGAG GVGLAAPQVG
60 70 80 90 100
RTVRVFVVDV EHHVRAFINP QITAASEEQS SYEEGCLSIP HIYERVLRPR
110 120 130 140 150
RVSVQYLDEN GKRCAVDADG ILARVIQHEY DHLDGILFLD RIDEKRRDDA
160
LRRYAALRGT IR
Length:162
Mass (Da):18,323
Last modified:November 1, 1998 - v1
Checksum:i15AEA6C940819CC1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000520 Genomic DNA. Translation: AAC65724.1.
PIRiH71284.
RefSeqiNP_219194.1. NC_000919.1.
WP_010882202.1. NC_021490.2.
YP_008091586.1. NC_021490.2.

Genome annotation databases

EnsemblBacteriaiAAC65724; AAC65724; TP_0757.
GeneIDi2611341.
KEGGitpa:TP0757.
tpw:TPANIC_0757.
PATRICi20531603. VBITrePal57110_0801.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000520 Genomic DNA. Translation: AAC65724.1.
PIRiH71284.
RefSeqiNP_219194.1. NC_000919.1.
WP_010882202.1. NC_021490.2.
YP_008091586.1. NC_021490.2.

3D structure databases

ProteinModelPortaliO83738.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO83738. 40 interactions.
MINTiMINT-6481412.
STRINGi243276.TP0757.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC65724; AAC65724; TP_0757.
GeneIDi2611341.
KEGGitpa:TP0757.
tpw:TPANIC_0757.
PATRICi20531603. VBITrePal57110_0801.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiIRSAEWY.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciTPAL243276:GC1H-803-MONOMER.

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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Nichols.

Entry informationi

Entry nameiDEF_TREPA
AccessioniPrimary (citable) accession number: O83738
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: November 1, 1998
Last modified: May 27, 2015
This is version 96 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

Complete proteome, Reference proteome

Documents

  1. 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.