Skip Header

Contribute Send feedback
Read comments (?) or add your own

B2KD65 (DEF_ELUMP) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 37. 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
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:Emin_0906
OrganismElusimicrobium minutum (strain Pei191) [Complete proteome] [HAMAP]
Taxonomic identifier445932 [NCBI]
Taxonomic lineageBacteria › Elusimicrobia › Elusimicrobia › Elusimicrobiales › Elusimicrobiaceae › Elusimicrobium ›

Protein attributes

Sequence length176 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.

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: HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 176176Peptide deformylase HAMAP-Rule MF_00163
PRO_1000097309

Sites

Active site1431 By similarity
Metal binding1001Iron By similarity
Metal binding1421Iron By similarity
Metal binding1461Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
B2KD65 [UniParc].

Last modified June 10, 2008. Version 1.
Checksum: 3FB5719DA52BD690

FASTA17619,873
        10         20         30         40         50         60 
MAVRRIVKYG EDILRQKLKP VDFKTLEPQL DAILQDMHDT CMSFQGAGLS ANQIGLTHRI 

        70         80         90        100        110        120 
AMIFIPEKTP KGEAQKFKRY VVINPVIVSK KGCVTDEEGC LSLPGLWVEI ERAESIVVHC 

       130        140        150        160        170 
LNEKGLPVEI HAKGFLAKAL QHEIDHLDGK IFIDHADPKL KPEIKKELKK LSKNWS

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001055 Genomic DNA. Translation: ACC98461.1.
RefSeqYP_001875798.1. NC_010644.1.

3D structure databases

ModBaseSearch...

Protein-protein interaction databases

STRING445932.Emin_0906.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACC98461; ACC98461; Emin_0906.
GeneID6262636.
KEGGemi:Emin_0906.
PATRIC21849040. VBIEluMin86178_0948.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAWVEIERA.

Enzyme and pathway databases

BioCycEMIN445932:GHM0-940-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. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_ELUMP
AccessionPrimary (citable) accession number: B2KD65
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: May 1, 2013
This is version 37 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

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents