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B2K504 (DEF_YERPB) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 38. 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:YPTS_3857
OrganismYersinia pseudotuberculosis serotype IB (strain PB1/+) [Complete proteome] [HAMAP]
Taxonomic identifier502801 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia

Protein attributes

Sequence length170 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 – 170170Peptide deformylase HAMAP-Rule MF_00163
PRO_1000097363

Sites

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

Sequences

Sequence LengthMass (Da)Tools
B2K504 [UniParc].

Last modified June 10, 2008. Version 1.
Checksum: EB01048E0E2423A7

FASTA17019,391
        10         20         30         40         50         60 
MSVLQVLHYP DERLRKIAAP VKEVNGEIQR IVDDMFETMY AEEGIGLAAT QVDVHQQIIV 

        70         80         90        100        110        120 
IDISENRDQR LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE 

       130        140        150        160        170 
LETDGLLAIC IQHEMDHLIG KLFVDYLSPL KRQRIRQKLE KMAKLNARAN 

« Hide

References

[1]"Complete sequence of Yersinia pseudotuberculosis PB1/+."
Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Munk A.C., Brettin T., Detter J.C., Han C., Tapia R., Schmutz J., Larimer F., Land M., Hauser L. expand/collapse author list , Challacombe J.F., Green L., Lindler L.E., Nikolich M.P., Richardson P.
Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: PB1/+.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001048 Genomic DNA. Translation: ACC90806.1.
RefSeqYP_001874263.1. NC_010634.1.

3D structure databases

ProteinModelPortalB2K504.
SMRB2K504. Positions 2-169.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING502801.YPTS_3857.

Proteomic databases

PRIDEB2K504.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACC90806; ACC90806; YPTS_3857.
GeneID6260484.
KEGGypb:YPTS_3857.
PATRIC18655996. VBIYerPse20639_4179.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAMAETMYE.
OrthoDBEOG664CMF.
ProtClustDBPRK00150.

Enzyme and pathway databases

BioCycYPSE502801:GHIH-3998-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_YERPB
AccessionPrimary (citable) accession number: B2K504
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: February 19, 2014
This is version 38 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