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B6JJP8 (DEF_OLICO) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 24. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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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:OCAR_7540, OCA5_c06000
OrganismOligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5) [Complete proteome] [HAMAP]
Taxonomic identifier504832 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Oligotropha

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 MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP 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-KW

   Molecular functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 171171Peptide deformylase HAMAP MF_00163
PRO_1000097327

Sites

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

Sequences

Sequence LengthMass (Da)Tools
B6JJP8 [UniParc].

Last modified December 16, 2008. Version 1.
Checksum: EB0D04A8BF41330E

FASTA17119,367
        10         20         30         40         50         60 
MAIREIISIP DKRLRRVSEP VEKITSEVRA LAEDMFETMY DAPGIGLAAI QVAVPLRLIT 

        70         80         90        100        110        120 
MDLAKKEGES APRVFINPEI LSKSEDIAVY EEGCLSIPEY YEEVERPASV RVRFMDLEGE 

       130        140        150        160        170 
VHEEDAEGLF ATCIQHEIDH LNGVLFIDYL SKLKRDRVMK KFTKAAKLAA K

« Hide

References

[1]"Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T."
Paul D., Bridges S., Burgess S.C., Dandass Y., Lawrence M.L.
J. Bacteriol. 190:5531-5532(2008) [PubMed: 18539730] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 49405 / DSM 1227 / OM5.
[2]"Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5."
Volland S., Rachinger M., Strittmatter A., Daniel R., Gottschalk G., Meyer O.
J. Bacteriol. 193:5043-5043(2011) [PubMed: 21742883] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 49405 / DSM 1227 / OM5.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001196 Genomic DNA. Translation: ACI94642.1.
CP002826 Genomic DNA. Translation: AEI05324.1.
RefSeqYP_002290507.1. NC_011386.1.
YP_004631565.1. NC_015684.1.

3D structure databases

ProteinModelPortalB6JJP8.
SMRB6JJP8. Positions 2-170.
ModBaseSearch...

Protein-protein interaction databases

STRINGB6JJP8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID10845732.
6990043.
GenomeReviewsGene locus OCAR_7540 in contig CP001196_GR.
KEGGoca:OCAR_7540.
PATRIC22808857. VBIOliCar134280_3371.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG665227.
OMAQKIVDDM.
ProtClustDBPRK00150.

Family and domain databases

HAMAPMF_00163. Pep_deformylase.
[Tree]
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
KOK01462.
PANTHERPTHR10458. Fmet_deformylase. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. Pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_OLICO
AccessionPrimary (citable) accession number: B6JJP8
Secondary accession number(s): F8BWX2
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: December 16, 2008
Last modified: January 25, 2012
This is version 24 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

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