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C1B0D9 (DEF_RHOOB) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 34. 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:ROP_18920
OrganismRhodococcus opacus (strain B4) [Complete proteome] [HAMAP]
Taxonomic identifier632772 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeRhodococcus

Protein attributes

Sequence length196 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 – 196196Peptide deformylase HAMAP-Rule MF_00163
PRO_1000200743

Sites

Active site1461 By similarity
Metal binding1031Iron By similarity
Metal binding1451Iron By similarity
Metal binding1491Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
C1B0D9 [UniParc].

Last modified May 26, 2009. Version 1.
Checksum: 5A16BF65861F2F64

FASTA19621,290
        10         20         30         40         50         60 
MAILPIRIVG DPVLHEPTET VSESPAELSE LIADMYDTMD AANGVGLAAN QVGIPLRLFV 

        70         80         90        100        110        120 
YDCPDVDETG KPFRRRGCVV NPVLETSERP ETMPDPDDDV EGCLSVPGEQ FPTGRAEWAK 

       130        140        150        160        170        180 
VTGTDADGNA VEIEGRDFFA RMLQHEVGHL DGFLYVDMLV GRNARAAKKT IKRAGWGVPG 

       190 
LSWVPGTVED PFGHDD 

« Hide

References

[1]"Comparison of the complete genome sequences of Rhodococcus erythropolis PR4 and Rhodococcus opacus B4."
Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S., Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.
Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: B4.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP011115 Genomic DNA. Translation: BAH50139.1.
RefSeqYP_002779084.1. NC_012522.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING632772.ROP_18920.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAH50139; BAH50139; ROP_18920.
GeneID7743285.
KEGGrop:ROP_18920.
PATRIC23221025. VBIRhoOpa21106_1907.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243508.
KOK01462.
OMADMYDTMD.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycROPA632772:GH0Q-1916-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_RHOOB
AccessionPrimary (citable) accession number: C1B0D9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 2009
Last modified: May 14, 2014
This is version 34 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