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Protein

Peptide deformylase

Gene

def

Organism
Dichelobacter nodosus (strain VCS1703A)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi103 – 1031IronUniRule annotation
Metal bindingi145 – 1451IronUniRule annotation
Active sitei146 – 1461UniRule annotation
Metal bindingi149 – 1491IronUniRule annotation

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

BioCyciDNOD246195:GHHS-156-MONOMER.

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:DNO_0156
OrganismiDichelobacter nodosus (strain VCS1703A)
Taxonomic identifieri246195 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaCardiobacterialesCardiobacteriaceaeDichelobacter
ProteomesiUP000000248 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 181181Peptide deformylasePRO_0000301027Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi246195.DNO_0156.

Structurei

3D structure databases

ProteinModelPortaliA5EWL8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
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.

A5EWL8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIYSILIHP DPRLRLPAQP VTHFDDALAE IVQNMYETMY HFHGIGLAAP
60 70 80 90 100
QVNIQQRLIV MDVPQRSAEE GEKAEQIPSD KLVLVNPEIV QRSEECQDYE
110 120 130 140 150
EGCLSLPNQY ALVTRPANIT VRYQDITGAT QERAAQGLLS VCIQHEIDHL
160 170 180
NGGLFIDHLS RLKRERLEKK LAKSLKNTKK S
Length:181
Mass (Da):20,521
Last modified:June 12, 2007 - v1
Checksum:i5B462AF9E02A7A4A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000513 Genomic DNA. Translation: ABQ13795.1.
RefSeqiWP_011927907.1. NC_009446.1.

Genome annotation databases

EnsemblBacteriaiABQ13795; ABQ13795; DNO_0156.
KEGGidno:DNO_0156.
PATRICi21784608. VBIDicNod48475_0156.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000513 Genomic DNA. Translation: ABQ13795.1.
RefSeqiWP_011927907.1. NC_009446.1.

3D structure databases

ProteinModelPortaliA5EWL8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246195.DNO_0156.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ13795; ABQ13795; DNO_0156.
KEGGidno:DNO_0156.
PATRICi21784608. VBIDicNod48475_0156.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciDNOD246195:GHHS-156-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: VCS1703A.

Entry informationi

Entry nameiDEF_DICNV
AccessioniPrimary (citable) accession number: A5EWL8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: June 12, 2007
Last modified: July 22, 2015
This is version 54 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.