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Protein

Peptide deformylase

Gene

def

Organism
Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (Clostridium acetobutylicum)
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 (By similarity).By similarity

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi85 – 851IronBy similarity
Metal bindingi126 – 1261IronBy similarity
Active sitei127 – 1271By similarity
Metal bindingi130 – 1301IronBy similarity

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

BioCyciCBEI290402:GHL5-3610-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Synonyms:fms
Ordered Locus Names:Cbei_3511
OrganismiClostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (Clostridium acetobutylicum)
Taxonomic identifieri290402 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium
ProteomesiUP000000565 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 136136Peptide deformylasePRO_0000082768Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi290402.Cbei_3511.

Structurei

3D structure databases

ProteinModelPortaliO08450.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiYETEESC.
OrthoDBiEOG6FNHTX.

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.

O08450-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIKPIVKDIL FLGQKSEEAT KNDMVVIDDL IDTLRANLEH CVGLAANMIG
60 70 80 90 100
VKKRILVFTV GNLIVPMINP VILKKEKPYE TEESCLSLIG FRKTKRYETI
110 120 130
EVTYLDRNFN KKKQVFNGFT AQIIQHEMDH FEGIII
Length:136
Mass (Da):15,623
Last modified:June 30, 1997 - v1
Checksum:i7E9CE063FFDE9BE6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z96934 Genomic DNA. Translation: CAB09662.1.
CP000721 Genomic DNA. Translation: ABR35634.1.
RefSeqiWP_012059684.1. NC_009617.1.
YP_001310590.1. NC_009617.1.

Genome annotation databases

EnsemblBacteriaiABR35634; ABR35634; Cbei_3511.
KEGGicbe:Cbei_3511.
PATRICi19351248. VBICloBei69853_3642.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z96934 Genomic DNA. Translation: CAB09662.1.
CP000721 Genomic DNA. Translation: ABR35634.1.
RefSeqiWP_012059684.1. NC_009617.1.
YP_001310590.1. NC_009617.1.

3D structure databases

ProteinModelPortaliO08450.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi290402.Cbei_3511.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR35634; ABR35634; Cbei_3511.
KEGGicbe:Cbei_3511.
PATRICi19351248. VBICloBei69853_3642.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiYETEESC.
OrthoDBiEOG6FNHTX.

Enzyme and pathway databases

BioCyciCBEI290402:GHL5-3610-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

« Hide 'large scale' publications
  1. "Truncation of peptide deformylase reduces the growth rate and stabilizes solvent production in Clostridium beijerinckii NCIMB 8052."
    Evans V.J., Liyanage H., Ravagnani A., Young M., Kashket E.R.
    Appl. Environ. Microbiol. 64:1780-1785(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51743 / NCIMB 8052.

Entry informationi

Entry nameiDEF_CLOB8
AccessioniPrimary (citable) accession number: O08450
Secondary accession number(s): A6LZ54
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 14, 1999
Last sequence update: June 30, 1997
Last modified: March 31, 2015
This is version 89 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.