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O08450 (DEF_CLOB8) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 79. 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
Synonyms:fms
Ordered Locus Names:Cbei_3511
OrganismClostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (Clostridium acetobutylicum) [Complete proteome] [HAMAP]
Taxonomic identifier290402 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium ›

Protein attributes

Sequence length136 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.

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: HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 136136Peptide deformylase HAMAP-Rule MF_00163
PRO_0000082768

Sites

Active site1271 By similarity
Metal binding851Iron By similarity
Metal binding1261Iron By similarity
Metal binding1301Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
O08450 [UniParc].

Last modified July 1, 1997. Version 1.
Checksum: 7E9CE063FFDE9BE6

FASTA13615,623
        10         20         30         40         50         60 
MIKPIVKDIL FLGQKSEEAT KNDMVVIDDL IDTLRANLEH CVGLAANMIG VKKRILVFTV 

        70         80         90        100        110        120 
GNLIVPMINP VILKKEKPYE TEESCLSLIG FRKTKRYETI EVTYLDRNFN KKKQVFNGFT 

       130 
AQIIQHEMDH FEGIII

« Hide

References

« Hide 'large scale' references
[1]"Truncation of peptide deformylase reduces the growth rate and stabilizes solvent production in Clostridium beijerinckii NCIMB 8052."
Evans V.J., Liyanage H., Ravagnani A., Young M., Kashket E.R.
Appl. Environ. Microbiol. 64:1780-1785(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete sequence of Clostridium beijerinckii NCIMB 8052."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Sims D., Brettin T., Bruce D., Tapia R., Brainard J., Schmutz J., Larimer F. expand/collapse author list , Land M., Hauser L., Kyrpides N., Mikhailova N., Bennet G., Cann I., Chen J.-S., Contreras A.L., Jones D., Kashket E., Mitchell W., Stoddard S., Schwarz W., Qureshi N., Young M., Shi Z., Ezeji T., White B., Blaschek H., Richardson P.
Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 51743 / NCIMB 8052.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		Z96934 Genomic DNA. Translation: CAB09662.1.
CP000721 Genomic DNA. Translation: ABR35634.1.
RefSeqYP_001310590.1. NC_009617.1.

3D structure databases

ProteinModelPortalO08450.
ModBaseSearch...

Protein-protein interaction databases

STRING290402.Cbei_3511.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABR35634; ABR35634; Cbei_3511.
GeneID5294680.
KEGGcbe:Cbei_3511.
PATRIC19351248. VBICloBei69853_3642.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAYETEESC.
ProtClustDBPRK09218.

Enzyme and pathway databases

BioCycCBEI290402:GHL5-3650-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. Fmet_deformylase. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_CLOB8
AccessionPrimary (citable) accession number: O08450
Secondary accession number(s): A6LZ54
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: July 1, 1997
Last modified: May 1, 2013
This is version 79 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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