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Protein

Peptide deformylase 1

Gene

def1

Organism
Bifidobacterium longum (strain NCC 2705)
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 bindingi129 – 1291IronUniRule annotation
Metal bindingi171 – 1711IronUniRule annotation
Active sitei172 – 1721UniRule annotation
Metal bindingi175 – 1751IronUniRule 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

BioCyciBLON206672:GI1E-853-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
Ordered Locus Names:BL1186
OrganismiBifidobacterium longum (strain NCC 2705)
Taxonomic identifieri206672 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeBifidobacterialesBifidobacteriaceaeBifidobacterium
ProteomesiUP000000439: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 217217Peptide deformylase 1PRO_0000082742Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi206672.BL1186.

Structurei

3D structure databases

ProteinModelPortaliQ8G534.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.
PhylomeDBiQ8G534.

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.

Sequencei

Sequence statusi: Complete.

Q8G534-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFGKNAKVDL ELNRDVEQLI KTGGKEKLLP IVQAGEPVLR QRTVAYNGQL
60 70 80 90 100
SKRTLAKLID TMHTTMLEAP GVGLAATQIG LGLALAVVED HVRDDEDDPR
110 120 130 140 150
EIAEFPFHVI INPSYKPTSD KTASFYEGCL SFDGYQAVRK RWLDITAEWD
160 170 180 190 200
DEDGKHHSEP LHGWPARIFQ HETDHLSGEL YIDRAEIRSL TTNENLEDYW
210
CEDPVPTEAA EELGFAL
Length:217
Mass (Da):24,443
Last modified:March 1, 2003 - v1
Checksum:i52F5B469B6F47163
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014295 Genomic DNA. Translation: AAN24991.1.
RefSeqiNP_696355.1. NC_004307.2.

Genome annotation databases

EnsemblBacteriaiAAN24991; AAN24991; BL1186.
GeneIDi1022716.
KEGGiblo:BL1186.
PATRICi21118873. VBIBifLon107831_0899.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014295 Genomic DNA. Translation: AAN24991.1.
RefSeqiNP_696355.1. NC_004307.2.

3D structure databases

ProteinModelPortaliQ8G534.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi206672.BL1186.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN24991; AAN24991; BL1186.
GeneIDi1022716.
KEGGiblo:BL1186.
PATRICi21118873. VBIBifLon107831_0899.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.
PhylomeDBiQ8G534.

Enzyme and pathway databases

BioCyciBLON206672:GI1E-853-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.
ProtoNetiSearch...

Publicationsi

  1. "The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract."
    Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., Zwahlen M.-C., Desiere F., Bork P., Delley M., Pridmore R.D., Arigoni F.
    Proc. Natl. Acad. Sci. U.S.A. 99:14422-14427(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NCC 2705.

Entry informationi

Entry nameiDEF1_BIFLO
AccessioniPrimary (citable) accession number: Q8G534
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: March 1, 2003
Last modified: January 7, 2015
This is version 64 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.