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Protein

Peptide deformylase

Gene

def

Organism
Lactobacillus fermentum (strain NBRC 3956 / LMG 18251)
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 bindingi116 – 1161IronUniRule annotation
Metal bindingi159 – 1591IronUniRule annotation
Active sitei160 – 1601UniRule annotation
Metal bindingi163 – 1631IronUniRule annotation

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciLFER334390:GJ2S-643-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:LAF_0599
OrganismiLactobacillus fermentum (strain NBRC 3956 / LMG 18251)
Taxonomic identifieri334390 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
ProteomesiUP000001697: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 189189Peptide deformylasePRO_1000097319Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi334390.LAF_0599.

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.

B2GBA3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MILMKDIVRD DQEGTVLRDY AAKVSFPLTE EEQQLAKDLM EYLEISQDEE
60 70 80 90 100
LAEKYGLRAG VGLAAPQVNV SKQMAAVLVP SDDEEDDTPI FKDVIINPVI
110 120 130 140 150
ISESVQMGAL TEGEGCLSVD RDIAGYVPRH DRITLKYQDV QGETHKVRLK
160 170 180
HYPAIVCQHE IDHLHGVLFY DHINKDNPFE APEGTVFFG
Length:189
Mass (Da):21,240
Last modified:June 10, 2008 - v1
Checksum:i9C1F7E60ECA3172B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008937 Genomic DNA. Translation: BAG26935.1.
RefSeqiYP_001843415.1. NC_010610.1.

Genome annotation databases

EnsemblBacteriaiBAG26935; BAG26935; LAF_0599.
GeneIDi6231795.
KEGGilfe:LAF_0599.
PATRICi22225316. VBILacFer15497_0645.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008937 Genomic DNA. Translation: BAG26935.1.
RefSeqiYP_001843415.1. NC_010610.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi334390.LAF_0599.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAG26935; BAG26935; LAF_0599.
GeneIDi6231795.
KEGGilfe:LAF_0599.
PATRICi22225316. VBILacFer15497_0645.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

Enzyme and pathway databases

BioCyciLFER334390:GJ2S-643-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. "Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production."
    Morita H., Toh H., Fukuda S., Horikawa H., Oshima K., Suzuki T., Murakami M., Hisamatsu S., Kato Y., Takizawa T., Fukuoka H., Yoshimura T., Itoh K., O'Sullivan D.J., McKay L.L., Ohno H., Kikuchi J., Masaoka T., Hattori M.
    DNA Res. 15:151-161(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NBRC 3956 / LMG 18251.

Entry informationi

Entry nameiDEF_LACF3
AccessioniPrimary (citable) accession number: B2GBA3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: January 7, 2015
This is version 42 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.