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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)DescriptionActionsGraphical viewLength
Metal bindingi123IronUniRule annotation1
Metal bindingi167IronUniRule annotation1
Active sitei168UniRule annotation1
Metal bindingi171IronUniRule 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:UPA3_0484
OrganismiUreaplasma parvum serovar 3 (strain ATCC 27815 / 27 / NCTC 11736)
Taxonomic identifieri505682 [NCBI]
Taxonomic lineageiBacteriaTenericutesMollicutesMycoplasmataceaeUreaplasma

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000769541 – 198Peptide deformylaseAdd BLAST198

Structurei

3D structure databases

ProteinModelPortaliB1AJA6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000243507.
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.

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.

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.

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

HOGENOMiHOG000243507.
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.
ProtoNetiSearch...

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: November 2, 2016
This is version 59 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

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.