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Protein

Peptide deformylase

Gene

def

Organism
Lactobacillus reuteri (strain JCM 1112)
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 bindingi113 – 1131IronUniRule annotation
Metal bindingi156 – 1561IronUniRule annotation
Active sitei157 – 1571UniRule annotation
Metal bindingi160 – 1601IronUniRule 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

BioCyciLREU557433:GHNR-654-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:LAR_0607
OrganismiLactobacillus reuteri (strain JCM 1112)
Taxonomic identifieri557433 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
ProteomesiUP000009150 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 186186Peptide deformylasePRO_1000097320Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi557433.LAR_0607.

Structurei

3D structure databases

ProteinModelPortaliB2G6P1.
SMRiB2G6P1. Positions 1-181.
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.

B2G6P1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYLMKDITRD GNPVLRKRAA KVSFPLSDED QKLAKDMMKY LEVSQDPELC
60 70 80 90 100
KKYKLRAGVG LAAPQVGVSK QMAAVLVPAP DEDEKPLFKD VIINPVIVSE
110 120 130 140 150
SVQYGALTEG EGCLSVDKDV PGYVPRHDRI TLRYQDVNGE THKVRLKHYP
160 170 180
AIVCQHEIDH LHGVLFYDHI NKDQPFEAPA DTVMIS
Length:186
Mass (Da):20,898
Last modified:June 10, 2008 - v1
Checksum:iE2D4ACC7B46888BD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP007281 Genomic DNA. Translation: BAG25123.1.
RefSeqiWP_003668269.1. NC_010609.1.
YP_001841603.1. NC_010609.1.

Genome annotation databases

EnsemblBacteriaiBAG25123; BAG25123; LAR_0607.
GeneIDi5189677.
KEGGilrf:LAR_0607.
PATRICi22258555. VBILacReu111271_0650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP007281 Genomic DNA. Translation: BAG25123.1.
RefSeqiWP_003668269.1. NC_010609.1.
YP_001841603.1. NC_010609.1.

3D structure databases

ProteinModelPortaliB2G6P1.
SMRiB2G6P1. Positions 1-181.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi557433.LAR_0607.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAG25123; BAG25123; LAR_0607.
GeneIDi5189677.
KEGGilrf:LAR_0607.
PATRICi22258555. VBILacReu111271_0650.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

Enzyme and pathway databases

BioCyciLREU557433:GHNR-654-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: JCM 1112.

Entry informationi

Entry nameiDEF_LACRJ
AccessioniPrimary (citable) accession number: B2G6P1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: May 27, 2015
This is version 45 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

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.