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Protein

Peptide deformylase

Gene

def

Organism
Lactobacillus sakei subsp. sakei (strain 23K)
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 bindingi112 – 1121IronUniRule annotation
Metal bindingi155 – 1551IronUniRule annotation
Active sitei156 – 1561UniRule annotation
Metal bindingi159 – 1591IronUniRule annotation

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:LCA_1087
OrganismiLactobacillus sakei subsp. sakei (strain 23K)
Taxonomic identifieri314315 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
ProteomesiUP000002707 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 185185Peptide deformylasePRO_0000301048Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi314315.LSA1087.

Structurei

3D structure databases

ProteinModelPortaliQ38WP3.
SMRiQ38WP3. Positions 1-185.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
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.

Q38WP3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILMKDIIRE GNPTLREIAQ PVSFPLSDED RQLAADMMTF LENSQDPEIA
60 70 80 90 100
AKYQLRAGVG LAAPQVDVSK QMSAVLVPGP EGEAPILKDV IINPKIISHS
110 120 130 140 150
VQDAALAEGE GCLSVDREVP GYVPRHDRIT LRYQDVEGVS HKIRLKNYPA
160 170 180
IVCQHEIDHL NGILFFDHIN KENPFAAPDD MIILE
Length:185
Mass (Da):20,530
Last modified:November 22, 2005 - v1
Checksum:i026C90177E5CE2C5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR936503 Genomic DNA. Translation: CAI55388.1.
RefSeqiWP_011374787.1. NC_007576.1.
YP_395697.1. NC_007576.1.

Genome annotation databases

EnsemblBacteriaiCAI55388; CAI55388; LCA_1087.
KEGGilsa:LSA1087.
PATRICi22274980. VBILacSak116432_1056.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR936503 Genomic DNA. Translation: CAI55388.1.
RefSeqiWP_011374787.1. NC_007576.1.
YP_395697.1. NC_007576.1.

3D structure databases

ProteinModelPortaliQ38WP3.
SMRiQ38WP3. Positions 1-185.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi314315.LSA1087.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAI55388; CAI55388; LCA_1087.
KEGGilsa:LSA1087.
PATRICi22274980. VBILacSak116432_1056.

Phylogenomic databases

eggNOGiCOG0242.
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.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 23K.

Entry informationi

Entry nameiDEF_LACSS
AccessioniPrimary (citable) accession number: Q38WP3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: November 22, 2005
Last modified: May 27, 2015
This is version 60 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.