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Q1C2X9 (DEF_YERPA) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 56. 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:YPA_3231
OrganismYersinia pestis bv. Antiqua (strain Antiqua) [Complete proteome] [HAMAP]
Taxonomic identifier360102 [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_0000301127

Sites

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

Sequences

Sequence LengthMass (Da)Tools
Q1C2X9 [UniParc].

Last modified July 11, 2006. 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 genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen."
Chain P.S.G., Hu P., Malfatti S.A., Radnedge L., Larimer F., Vergez L.M., Worsham P., Chu M.C., Andersen G.L.
J. Bacteriol. 188:4453-4463(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Antiqua.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000308 Genomic DNA. Translation: ABG15193.1.
RefSeqYP_653138.1. NC_008150.1.

3D structure databases

ProteinModelPortalQ1C2X9.
SMRQ1C2X9. Positions 2-169.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING360102.YPA_3231.

Proteomic databases

PRIDEQ1C2X9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABG15193; ABG15193; YPA_3231.
GeneID4118500.
KEGGypa:YPA_3231.
PATRIC18586314. VBIYerPes1796_3952.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAELLAICI.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycYPES360102:GHZU-3301-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_YERPA
AccessionPrimary (citable) accession number: Q1C2X9
Entry history
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: July 11, 2006
Last modified: May 14, 2014
This is version 56 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