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Protein

Peptide deformylase

Gene

def

Organism
Lactobacillus brevis (strain ATCC 367 / JCM 1170)
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 bindingi113IronUniRule annotation1
Metal bindingi156IronUniRule annotation1
Active sitei157UniRule annotation1
Metal bindingi160IronUniRule 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:LVIS_1411
OrganismiLactobacillus brevis (strain ATCC 367 / JCM 1170)
Taxonomic identifieri387344 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
Proteomesi
  • UP000001652 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003010421 – 186Peptide deformylaseAdd BLAST186

Interactioni

Protein-protein interaction databases

STRINGi387344.LVIS_1411.

Structurei

3D structure databases

ProteinModelPortaliQ03QL3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
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.

Q03QL3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFLMKDIVRD GDPVLRQEAA DVTFPLSEED QQLAKDLMEY LVVSQDPEQC
60 70 80 90 100
KKYGLRAGVG LAAPQVGVSK KMASVLVPPV EEDGKSPFTD VIINPVIISE
110 120 130 140 150
SVQAGALTEG EGCLSVDKDV PGFVPRHDRI TLRYYDVNGE KHQVRLKNYP
160 170 180
AIVCQHEIDH LHGTLFYDHI NKDQPFSRDD DMIMIE
Length:186
Mass (Da):20,837
Last modified:November 14, 2006 - v1
Checksum:iF02C35D243C1AF77
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000416 Genomic DNA. Translation: ABJ64509.1.
RefSeqiWP_011668082.1. NC_008497.1.

Genome annotation databases

EnsemblBacteriaiABJ64509; ABJ64509; LVIS_1411.
GeneIDi4413358.
KEGGilbr:LVIS_1411.
PATRICi22201757. VBILacBre134470_1347.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000416 Genomic DNA. Translation: ABJ64509.1.
RefSeqiWP_011668082.1. NC_008497.1.

3D structure databases

ProteinModelPortaliQ03QL3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi387344.LVIS_1411.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABJ64509; ABJ64509; LVIS_1411.
GeneIDi4413358.
KEGGilbr:LVIS_1411.
PATRICi22201757. VBILacBre134470_1347.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
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_LACBA
AccessioniPrimary (citable) accession number: Q03QL3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: November 14, 2006
Last modified: November 2, 2016
This is version 67 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

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.