Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Peptide deformylase

Gene

def

Organism
Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg) (Lachnoclostridium phytofermentans)
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 bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule 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

BioCyciCPHY357809:GHCL-2532-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:Cphy_2492
OrganismiClostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg) (Lachnoclostridium phytofermentans)
Taxonomic identifieri357809 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesLachnospiraceae
ProteomesiUP000000370 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 163163Peptide deformylasePRO_1000076941Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi357809.Cphy_2492.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiDTMLEMD.
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.

A9KM99-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKRNIRIMG DSILNKTSKV IEEVTPKIDT LIDDMLDTMY DAGGVGLAAP
60 70 80 90 100
QVGVLKRLVV IDVSLEGNEP IILINPEIIS TDGEQTGDEG CLSLPGKAGI
110 120 130 140 150
VTRPNYVKVK AYDRHMKPFE VEGEGLLARA FCHEIDHLDG ILYVEKVNGE
160
VHEVTSYDEE EEE
Length:163
Mass (Da):17,951
Last modified:February 4, 2008 - v1
Checksum:iC9B074BD7CEAF046
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000885 Genomic DNA. Translation: ABX42853.1.
RefSeqiWP_012200506.1. NC_010001.1.
YP_001559592.1. NC_010001.1.

Genome annotation databases

EnsemblBacteriaiABX42853; ABX42853; Cphy_2492.
KEGGicpy:Cphy_2492.
PATRICi19504714. VBICloPhy16213_2595.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000885 Genomic DNA. Translation: ABX42853.1.
RefSeqiWP_012200506.1. NC_010001.1.
YP_001559592.1. NC_010001.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi357809.Cphy_2492.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABX42853; ABX42853; Cphy_2492.
KEGGicpy:Cphy_2492.
PATRICi19504714. VBICloPhy16213_2595.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiDTMLEMD.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciCPHY357809:GHCL-2532-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700394 / DSM 18823 / ISDg.

Entry informationi

Entry nameiDEF_CLOPH
AccessioniPrimary (citable) accession number: A9KM99
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 19, 2008
Last sequence update: February 4, 2008
Last modified: March 31, 2015
This is version 52 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.