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Q13F18 (DEF_RHOPS) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 50. 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:RPD_0081
OrganismRhodopseudomonas palustris (strain BisB5) [Complete proteome] [HAMAP]
Taxonomic identifier316057 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeRhodopseudomonas

Protein attributes

Sequence length175 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 – 175175Peptide deformylase HAMAP-Rule MF_00163
PRO_0000301089

Sites

Active site1391 By similarity
Metal binding961Iron By similarity
Metal binding1381Iron By similarity
Metal binding1421Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
Q13F18 [UniParc].

Last modified October 31, 2006. Version 1.
Checksum: 98C170300FE8832C

FASTA17519,687
        10         20         30         40         50         60 
MALREIIILP DKRLREISKP VAEVTPEIRK LADDMFESMY DAPGIGLAAI QIAEPVRLIT 

        70         80         90        100        110        120 
MDIVRKEGNG KSDPRAFINP EIVGASAEMN VYEEGCLSIP EYYADVERPA VVRIRYTDLD 

       130        140        150        160        170 
GNVKEEDADG LFATCIQHEI DHLDGVLFVD HLSKLKRAMV VRKFEKAAKR GIKYV 

« Hide

References

[1]"Complete sequence of Rhodopseudomonas palustris BisB5."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M. expand/collapse author list , Hauser L., Pelletier D.A., Kyrpides N., Lykidis A., Oda Y., Harwood C.S., Richardson P.
Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: BisB5.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000283 Genomic DNA. Translation: ABE37321.1.
RefSeqYP_567222.1. NC_007958.1.

3D structure databases

ProteinModelPortalQ13F18.
SMRQ13F18. Positions 2-171.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING316057.RPD_0081.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABE37321; ABE37321; RPD_0081.
GeneID4020536.
KEGGrpd:RPD_0081.
PATRIC23274961. VBIRhoPal120395_0079.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAWATCAQH.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycRPAL316057:GHDC-82-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_RHOPS
AccessionPrimary (citable) accession number: Q13F18
Entry history
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: October 31, 2006
Last modified: May 14, 2014
This is version 50 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