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B3DUG9 (DEF_METI4) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 39. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

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:Minf_0917
OrganismMethylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4)) [Complete proteome] [HAMAP]
Taxonomic identifier481448 [NCBI]
Taxonomic lineageBacteriaVerrucomicrobiaunclassified VerrucomicrobiaMethylacidiphilalesMethylacidiphilaceaeMethylacidiphilum

Protein attributes

Sequence length190 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-Rule MF_00163

Catalytic activity

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

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP-Rule 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-HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 190190Peptide deformylase HAMAP-Rule MF_00163
PRO_1000097323

Sites

Active site1491 By similarity
Metal binding1061Iron By similarity
Metal binding1481Iron By similarity
Metal binding1521Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
B3DUG9 [UniParc].

Last modified July 22, 2008. Version 1.
Checksum: 486AC49046D19A82

FASTA19021,388
        10         20         30         40         50         60 
MILKLVLYDN PILRKKGMPI DSFDDRLKRL VQDMLETMAY YKGVGLAAQQ VGLNLQLAVI 

        70         80         90        100        110        120 
DVSGSKLSSS LLIGGKPAMV EEHMPLFLIN PTLSYTQSKE ISNEGCLSFP GLRIDVPRSK 

       130        140        150        160        170        180 
RVKVKTFDLE GRPWYFEAGG FLSVAIQHEF DHLQGKLFID YLSAEQKKAI KEELEKIKRG 

       190 
EAILSVKETD 

« Hide

References

[1]"Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia."
Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F. expand/collapse author list , Feng L., Wang L., Alam M.
Biol. Direct 3:26-26(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Isolate V4.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000975 Genomic DNA. Translation: ACD82972.1.
RefSeqYP_001939570.1. NC_010794.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING481448.Minf_0917.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACD82972; ACD82972; Minf_0917.
GeneID6351842.
KEGGmin:Minf_0917.
PATRIC22490949. VBIMetInf111569_0970.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMATFIDNMF.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycMINF481448:GJEI-932-MONOMER.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_METI4
AccessionPrimary (citable) accession number: B3DUG9
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 22, 2008
Last modified: February 19, 2014
This is version 39 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