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C4K6Y0 (DEF_HAMD5) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 32. 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:HDEF_1720
OrganismHamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT) [Complete proteome] [HAMAP]
Taxonomic identifier572265 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeaphid secondary symbiontsCandidatus Hamiltonella

Protein attributes

Sequence length171 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 – 171171Peptide deformylase HAMAP-Rule MF_00163
PRO_1000203604

Sites

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

Sequences

Sequence LengthMass (Da)Tools
C4K6Y0 [UniParc].

Last modified July 7, 2009. Version 1.
Checksum: 2895AAEC85926923

FASTA17119,668
        10         20         30         40         50         60 
MSILQILHFP DDRLRKIASP VKKMDDQIRQ IADDMLETMY QAEGIGLAAT QVNIHQRIIV 

        70         80         90        100        110        120 
IDVSEDRHQP LILINPELLE KSGETGIEEG CLSIPGEKAF IPRAKEITIQ ALNREGRSFR 

       130        140        150        160        170 
LSADDLLAIC IQHEMDHLIG KLFVDYLSPF KRQRIQKKME KLQKINEKKD K 

« Hide

References

[1]"Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors."
Degnan P.H., Yu Y., Sisneros N., Wing R.A., Moran N.A.
Proc. Natl. Acad. Sci. U.S.A. 106:9063-9068(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 5AT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001277 Genomic DNA. Translation: ACQ68323.1.
RefSeqYP_002924471.1. NC_012751.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING572265.HDEF_1720.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACQ68323; ACQ68323; HDEF_1720.
GeneID7951317.
KEGGhde:HDEF_1720.
PATRIC31974899. VBICanHam112931_1710.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
KOK01462.
OMAPNQYAEV.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycHDEF572265:GJAB-1736-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_HAMD5
AccessionPrimary (citable) accession number: C4K6Y0
Entry history
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 7, 2009
Last modified: May 14, 2014
This is version 32 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