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Protein

Peptide deformylase

Gene

def

Organism
Elusimicrobium minutum (strain Pei191)
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 bindingi100 – 1001IronUniRule annotation
Metal bindingi142 – 1421IronUniRule annotation
Active sitei143 – 1431UniRule annotation
Metal bindingi146 – 1461IronUniRule annotation

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

BioCyciEMIN445932:GHM0-940-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:Emin_0906
OrganismiElusimicrobium minutum (strain Pei191)
Taxonomic identifieri445932 [NCBI]
Taxonomic lineageiBacteriaElusimicrobiaElusimicrobiaElusimicrobialesElusimicrobiaceaeElusimicrobium
ProteomesiUP000001029 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 176176Peptide deformylasePRO_1000097309Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi445932.Emin_0906.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
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.

B2KD65-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVRRIVKYG EDILRQKLKP VDFKTLEPQL DAILQDMHDT CMSFQGAGLS
60 70 80 90 100
ANQIGLTHRI AMIFIPEKTP KGEAQKFKRY VVINPVIVSK KGCVTDEEGC
110 120 130 140 150
LSLPGLWVEI ERAESIVVHC LNEKGLPVEI HAKGFLAKAL QHEIDHLDGK
160 170
IFIDHADPKL KPEIKKELKK LSKNWS
Length:176
Mass (Da):19,873
Last modified:June 10, 2008 - v1
Checksum:i3FB5719DA52BD690
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001055 Genomic DNA. Translation: ACC98461.1.
RefSeqiWP_012415076.1. NC_010644.1.
YP_001875798.1. NC_010644.1.

Genome annotation databases

EnsemblBacteriaiACC98461; ACC98461; Emin_0906.
KEGGiemi:Emin_0906.
PATRICi21849040. VBIEluMin86178_0948.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001055 Genomic DNA. Translation: ACC98461.1.
RefSeqiWP_012415076.1. NC_010644.1.
YP_001875798.1. NC_010644.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi445932.Emin_0906.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACC98461; ACC98461; Emin_0906.
KEGGiemi:Emin_0906.
PATRICi21849040. VBIEluMin86178_0948.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciEMIN445932:GHM0-940-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. "Genomic analysis of 'Elusimicrobium minutum,' the first cultivated representative of the phylum 'Elusimicrobia' (formerly termite group 1)."
    Herlemann D.P.R., Geissinger O., Ikeda-Ohtsubo W., Kunin V., Sun H., Lapidus A., Hugenholtz P., Brune A.
    Appl. Environ. Microbiol. 75:2841-2849(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Pei191.

Entry informationi

Entry nameiDEF_ELUMP
AccessioniPrimary (citable) accession number: B2KD65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: April 29, 2015
This is version 48 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.