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Protein

Peptide deformylase

Gene

def

Organism
Pediococcus pentosaceus (strain ATCC 25745 / 183-1w)
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 bindingi111 – 1111IronUniRule annotation
Metal bindingi154 – 1541IronUniRule annotation
Active sitei155 – 1551UniRule annotation
Metal bindingi158 – 1581IronUniRule 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

BioCyciPPEN278197:GI4Y-1159-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:PEPE_1159
OrganismiPediococcus pentosaceus (strain ATCC 25745 / 183-1w)
Taxonomic identifieri278197 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaePediococcus
ProteomesiUP000000773: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184Peptide deformylasePRO_0000301074Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi278197.PEPE_1159.

Structurei

3D structure databases

ProteinModelPortaliQ03F09.
SMRiQ03F09. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

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.

Q03F09-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIKMNDITRD GNPVLRKRAE KLTFPLDPKY LKVADEMMEY LKNSQDPAIA
60 70 80 90 100
EKYHLRAGVG LAAPQIGLSI QMASVLVPGP DNTIDLEETL VNPVIVSQSV
110 120 130 140 150
QIAALEEGEG CLSVDKDVPG YVPRHDRITV RYQTLDGEEK TIKLRDYPAI
160 170 180
VCQHEIDHLK GTLFYDHINK ENPLDIEDNA ILIG
Length:184
Mass (Da):20,575
Last modified:November 14, 2006 - v1
Checksum:i96A9615091FAFD84
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000422 Genomic DNA. Translation: ABJ68213.1.
RefSeqiYP_804655.1. NC_008525.1.

Genome annotation databases

EnsemblBacteriaiABJ68213; ABJ68213; PEPE_1159.
GeneIDi4417622.
KEGGippe:PEPE_1159.
PATRICi22875638. VBIPedPen34213_1102.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000422 Genomic DNA. Translation: ABJ68213.1.
RefSeqiYP_804655.1. NC_008525.1.

3D structure databases

ProteinModelPortaliQ03F09.
SMRiQ03F09. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi278197.PEPE_1159.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABJ68213; ABJ68213; PEPE_1159.
GeneIDi4417622.
KEGGippe:PEPE_1159.
PATRICi22875638. VBIPedPen34213_1102.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

Enzyme and pathway databases

BioCyciPPEN278197:GI4Y-1159-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 25745 / 183-1w.

Entry informationi

Entry nameiDEF_PEDPA
AccessioniPrimary (citable) accession number: Q03F09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: November 14, 2006
Last modified: January 7, 2015
This is version 54 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.