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Q5QXI5 (DEF_IDILO) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 42. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Peptide deformylase
Short name=PDF
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:def
Ordered Locus Names:IL0018
OrganismIdiomarina loihiensis (strain ATCC BAA-735 / DSM 15497 / L2-TR) [Complete proteome] [HAMAP]
Taxonomic identifier283942 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Alteromonadales › Idiomarinaceae › Idiomarina

Protein attributes

Sequence length174 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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. HAMAP MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP MF_00163

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processtranslation

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 174174Peptide deformylase HAMAP MF_00163
PRO_0000301041

Sites

Active site1341 By similarity
Metal binding911Iron By similarity
Metal binding1331Iron By similarity
Metal binding1371Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5QXI5 [UniParc].

Last modified January 4, 2005. Version 1.
Checksum: 1AEF4B79561150B4

FASTA17419,983
        10         20         30         40         50         60 
MAKMTVLQYP DERLRKVAQK IEKVDDNIRS VIDDMFETMY EEQGVGLAAT QVDVHRRLFV 

        70         80         90        100        110        120 
SDCSEDQNEP LVFINPEITE AEGHFKNDEG CLSFPGVYAK VERAERITVT ALDKNGERFS 

       130        140        150        160        170 
RSAEGLLAIC IQHEIDHLDG KLFVDYLSPL KRERIRKKLE KEQRLAEKQA AEAQ

« Hide

References

[1]"Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy."
Hou S., Saw J.H., Lee K.S., Freitas T.A., Belisle C., Kawarabayasi Y., Donachie S.P., Pikina A., Galperin M.Y., Koonin E.V., Makarova K.S., Omelchenko M.V., Sorokin A., Wolf Y.I., Li Q.X., Keum Y.S., Campbell S., Denery J. expand/collapse author list , Aizawa S., Shibata S., Malahoff A., Alam M.
Proc. Natl. Acad. Sci. U.S.A. 101:18036-18041(2004) [PubMed: 15596722] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-735 / DSM 15497 / L2-TR.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE017340 Genomic DNA. Translation: AAV80862.1.
RefSeqYP_154411.1. NC_006512.1.

3D structure databases

HSSPHSSP built from PDB template 1N5N based on UniProtKB Q9I7A8.
ProteinModelPortalQ5QXI5.
SMRQ5QXI5. Positions 2-165.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID3173153.
GenomeReviewsGene locus IL0018 in contig AE017340_GR.
KEGGilo:IL0018.
NMPDRfig|283942.3.peg.68.
PATRIC22138041. VBIIdiLoi21852_0018.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG665227.
OMAEIVSKQG.

Enzyme and pathway databases

BioCycILOI283942:IL0018-MONOMER.

Family and domain databases

HAMAPMF_00163. Pep_deformylase.
[Tree]
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
KOK01462.
PANTHERPTHR10458. Fmet_deformylase. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. Pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_IDILO
AccessionPrimary (citable) accession number: Q5QXI5
Entry history
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: January 4, 2005
Last modified: January 25, 2012
This is version 42 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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