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Q67PR5 (DEF_SYMTH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 63. 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:STH1343
OrganismSymbiobacterium thermophilum (strain T / IAM 14863) [Complete proteome] [HAMAP]
Taxonomic identifier292459 [NCBI]
Taxonomic lineageBacteriaFirmicutesClostridiaClostridialesClostridiales Family XVIII. Incertae SedisSymbiobacterium

Protein attributes

Sequence length217 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 – 217217Peptide deformylase HAMAP-Rule MF_00163
PRO_0000301114

Sites

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

Sequences

Sequence LengthMass (Da)Tools
Q67PR5 [UniParc].

Last modified October 11, 2004. Version 1.
Checksum: DAA0BEF5C915026C

FASTA21723,242
        10         20         30         40         50         60 
MAILEIVKEP AEVLRKKAKP VTKINASIRK LLDDMTETMY AAPGVGLAAP QVGVSKRLIV 

        70         80         90        100        110        120 
VDPQDGSGQL YQLINPEIVK AEGWVKGTEG CLSIPGMVGD VWRYEKVQVV ALDRTGKKVW 

       130        140        150        160        170        180 
IDAEGYLARI FQHEIDHLDG ILYTDKCTNL RPVSEDGEEE EEAEVAEVMP EPEAEGAGEP 

       190        200        210 
SAEGAGQAAA EAGAEEGEQV TTGVSGERRG SAAAKEE 

« Hide

References

[1]"Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism."
Ueda K., Yamashita A., Ishikawa J., Shimada M., Watsuji T., Morimura K., Ikeda H., Hattori M., Beppu T.
Nucleic Acids Res. 32:4937-4944(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: T / IAM 14863.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP006840 Genomic DNA. Translation: BAD40328.1.
RefSeqYP_075172.1. NC_006177.1.

3D structure databases

ProteinModelPortalQ67PR5.
SMRQ67PR5. Positions 1-149.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING292459.STH1343.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD40328; BAD40328; STH1343.
GeneID2979184.
KEGGsth:STH1343.
PATRIC23780837. VBISymThe116959_1339.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243508.
KOK01462.
OMANDPLILV.
OrthoDBEOG664CMF.

Enzyme and pathway databases

BioCycSTHE292459:GJMM-1412-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_SYMTH
AccessionPrimary (citable) accession number: Q67PR5
Entry history
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: October 11, 2004
Last modified: May 14, 2014
This is version 63 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