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Protein

Peptide deformylase

Gene

def

Organism
Ureaplasma parvum serovar 3 (strain ATCC 27815 / 27 / NCTC 11736)
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 bindingi123 – 1231IronUniRule annotation
Metal bindingi167 – 1671IronUniRule annotation
Active sitei168 – 1681UniRule annotation
Metal bindingi171 – 1711IronUniRule 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

BioCyciUPAR505682:GHAZ-487-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:UPA3_0484
OrganismiUreaplasma parvum serovar 3 (strain ATCC 27815 / 27 / NCTC 11736)
Taxonomic identifieri505682 [NCBI]
Taxonomic lineageiBacteriaTenericutesMollicutesMycoplasmataceaeUreaplasma

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 198198Peptide deformylasePRO_1000076954Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliB1AJA6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

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.

B1AJA6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYNIKFLDLL NSNLKPNPQW IFKDPHPILR EVTQDIEGNE LSKDDIYYLK
60 70 80 90 100
KMVRYIDVCY HNQAKKYKIR SGIAIAANQV GWNKRATYIH FNDEAKEHHY
110 120 130 140 150
LLINPHIIKR SSEIAYLNPG EGCLSVDDDR SGYVIRNKKV HVKAYDLISE
160 170 180 190
QFIDQEFSGI IAICIQHEIG HLDAGLYYDN INQQQPFYAD PSWTKIGR
Length:198
Mass (Da):23,143
Last modified:April 8, 2008 - v1
Checksum:i19F035D052625C95
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000942 Genomic DNA. Translation: ACA32898.1.
RefSeqiWP_010891784.1. NC_010503.1.
YP_001752550.1. NC_010503.1.

Genome annotation databases

EnsemblBacteriaiACA32898; ACA32898; UPA3_0484.
GeneIDi876337.
KEGGiupa:UPA3_0484.
PATRICi20533193. VBIUrePar123156_0473.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000942 Genomic DNA. Translation: ACA32898.1.
RefSeqiWP_010891784.1. NC_010503.1.
YP_001752550.1. NC_010503.1.

3D structure databases

ProteinModelPortaliB1AJA6.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA32898; ACA32898; UPA3_0484.
GeneIDi876337.
KEGGiupa:UPA3_0484.
PATRICi20533193. VBIUrePar123156_0473.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

Enzyme and pathway databases

BioCyciUPAR505682:GHAZ-487-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. "Genome sequence of Ureaplasma parvum serovar 3."
    Methe B.A., Glass J., Waites K., Shrivastava S.
    Submitted (FEB-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 27815 / 27 / NCTC 11736.

Entry informationi

Entry nameiDEF_UREP2
AccessioniPrimary (citable) accession number: B1AJA6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: April 8, 2008
Last modified: June 24, 2015
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.