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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

GO - Biological processi

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
Proteomesi
  • UP000000565 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

eggNOGiENOG4107YDN. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
KOiK01462.
OMAiHCNGILI.
OrthoDBiPOG091H02B0.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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:July 1, 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.

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.

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

eggNOGiENOG4107YDN. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243509.
KOiK01462.
OMAiHCNGILI.
OrthoDBiPOG091H02B0.

Enzyme and pathway databases

BioCyciCBEI290402:GHL5-3610-MONOMER.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

Entry informationi

Entry nameiDEF_CLOB8
AccessioniPrimary (citable) accession number: O08450
Secondary accession number(s): A6LZ54
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: July 1, 1997
Last modified: September 7, 2016
This is version 93 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

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 one 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.