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Protein

Peptide deformylase

Gene

def

Organism
Clostridium botulinum (strain Alaska E43 / Type E3)
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 bindingi88 – 881IronUniRule annotation
Metal bindingi130 – 1301IronUniRule annotation
Active sitei131 – 1311UniRule annotation
Metal bindingi134 – 1341IronUniRule 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

BioCyciCBOT508767:GHKO-1162-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:CLH_1166
OrganismiClostridium botulinum (strain Alaska E43 / Type E3)
Taxonomic identifieri508767 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium
ProteomesiUP000001738: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 147147Peptide deformylasePRO_1000097302Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi508767.CLH_1166.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiYVGEEGC.
OrthoDBiEOG664CMF.

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.

B2V4B1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALRNIRKYG DSVLRKKCRE VEKIDERLVT LIKDMLETMY DADGVGLAAP
60 70 80 90 100
QVGILKRLFI VDIGDGPLVF INPEILDTDG KQVDEEGCLS LPGKTEPVMR
110 120 130 140
PNYVKARALN EKGEEFEIEA EELLARAILH EYDHLNGTLF IDRTTKK
Length:147
Mass (Da):16,643
Last modified:July 1, 2008 - v1
Checksum:iDFC88062E4F68086
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001078 Genomic DNA. Translation: ACD52880.1.
RefSeqiYP_001920560.1. NC_010723.1.

Genome annotation databases

EnsemblBacteriaiACD52880; ACD52880; CLH_1166.
GeneIDi6318416.
KEGGicbt:CLH_1166.
PATRICi19418596. VBICloBot115804_1095.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001078 Genomic DNA. Translation: ACD52880.1.
RefSeqiYP_001920560.1. NC_010723.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi508767.CLH_1166.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD52880; ACD52880; CLH_1166.
GeneIDi6318416.
KEGGicbt:CLH_1166.
PATRICi19418596. VBICloBot115804_1095.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiYVGEEGC.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciCBOT508767:GHKO-1162-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. "Complete genome sequence of Clostridium botulinum E3 str. Alaska E43."
    Brinkac L.M., Brown J.L., Bruce D., Detter C., Munk C., Smith L.A., Smith T.J., Sutton G., Brettin T.S.
    Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Alaska E43 / Type E3.

Entry informationi

Entry nameiDEF_CLOBA
AccessioniPrimary (citable) accession number: B2V4B1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: January 7, 2015
This is version 43 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.