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P68826 (DEF_STAAU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 51. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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
Synonyms:def1, pdf1
OrganismStaphylococcus aureus
Taxonomic identifier1280 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesStaphylococcus

Protein attributes

Sequence length183 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

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.

Mass spectrometry

Molecular mass is 20600 Da from positions 1 - 183. Determined by MALDI. Ref.2

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
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 – 183183Peptide deformylase HAMAP-Rule MF_00163
PRO_0000082843

Sites

Active site1551 By similarity
Metal binding1111Iron
Metal binding1541Iron
Metal binding1581Iron

Secondary structure

............................. 183
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P68826 [UniParc].

Last modified December 21, 2004. Version 1.
Checksum: 32A64066A6FEAB0E

FASTA18320,559
        10         20         30         40         50         60 
MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA KRYGLRSGVG 

        70         80         90        100        110        120 
LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV QEAYLPTGEG CLSVDDNVAG 

       130        140        150        160        170        180 
LVHRHNRITI KAKDIEGNDI QLRLKGYPAI VFQHEIDHLN GVMFYDHIDK NHPLQPHTDA 


VEV 

« Hide

References

[1]"Staphylococcus aureus deformylase 1 encoding DNA."
Lonetto M.A., Sylvester D.R., Warren R.L.
Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: WCUH29 / NCIMB 40771.
[2]"Identification of Staphylococcus aureus proteins recognized by the antibody-mediated immune response to a biofilm infection."
Brady R.A., Leid J.G., Camper A.K., Costerton J.W., Shirtliff M.E.
Infect. Immun. 74:3415-3426(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY.
Strain: MRSA-M2.
[3]"Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase."
Kreusch A., Spraggon G., Lee C.C., Klock H., McMullan D., Ng K., Shin T., Vincent J., Warner I., Ericson C., Lesley S.A.
J. Mol. Biol. 330:309-321(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY007227 Genomic DNA. Translation: AAG02249.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1LM4X-ray1.45A/B1-183[»]
1LMHX-ray1.90A1-183[»]
1LQWX-ray1.87A/B1-183[»]
1Q1YX-ray1.90A1-183[»]
2AI9X-ray2.50A/B1-183[»]
ProteinModelPortalP68826.
SMRP68826. Positions 1-183.
ModBaseSearch...
MobiDBSearch...

Chemistry

BindingDBP68826.
ChEMBLCHEMBL2010635.

Proteomic databases

PRIDEP68826.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Phylogenomic databases

eggNOGCOG0242.

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...

Other

EvolutionaryTraceP68826.

Entry information

Entry nameDEF_STAAU
AccessionPrimary (citable) accession number: P68826
Secondary accession number(s): Q9F4L4
Entry history
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: December 21, 2004
Last modified: February 19, 2014
This is version 51 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references