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B0U4M4 (DEF_XYLFM) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 44. 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:Xfasm12_1929
OrganismXylella fastidiosa (strain M12) [Complete proteome] [HAMAP]
Taxonomic identifier405440 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella

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_1000097362

Sites

Active site1371 By similarity
Metal binding941Iron By similarity
Metal binding1361Iron By similarity
Metal binding1401Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
B0U4M4 [UniParc].

Last modified April 8, 2008. Version 1.
Checksum: F2CD729A4C733A5C

FASTA17019,158
        10         20         30         40         50         60 
MALLPILEFP DPRLRTKAVR VGVAEVVSSS FQTLLDDMFE TMYAAPGIGL AATQVNVHQR 

        70         80         90        100        110        120 
FMVVDVSEEK NAPMVFINPE IVTREGDQVF QEGCLSVPGI HADVTRALSI VVRFLDRHGD 

       130        140        150        160        170 
EQQLTAEGLL AVCIQHEMDH LDGKLFIDYL SPLKRDMVRR KLEKQRRRAS 

« Hide

References

[1]"Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California."
Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E.L.
J. Bacteriol. 192:4534-4534(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: M12.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000941 Genomic DNA. Translation: ACA12803.1.
RefSeqYP_001776433.1. NC_010513.1.

3D structure databases

ProteinModelPortalB0U4M4.
SMRB0U4M4. Positions 1-168.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING405440.Xfasm12_1929.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACA12803; ACA12803; Xfasm12_1929.
GeneID6120209.
KEGGxfm:Xfasm12_1929.
PATRIC24140646. VBIXylFas124301_2265.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAEETGEEW.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycXFAS405440:GH0D-1969-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_XYLFM
AccessionPrimary (citable) accession number: B0U4M4
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: May 14, 2014
This is version 44 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