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Protein

Peptide deformylase

Gene

def

Organism
Staphylococcus aureus
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi111 – 1111Iron
Metal bindingi154 – 1541Iron
Active sitei155 – 1551By similarity
Metal bindingi158 – 1581Iron

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BRENDAi3.5.1.88. 3352.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Synonyms:def1, pdf1
OrganismiStaphylococcus aureus
Taxonomic identifieri1280 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 183183Peptide deformylasePRO_0000082843Add
BLAST

Proteomic databases

PRIDEiP68826.

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL1100.

Structurei

Secondary structure

1
183
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63Combined sources
Helixi13 – 164Combined sources
Helixi28 – 4518Combined sources
Helixi47 – 537Combined sources
Beta strandi58 – 625Combined sources
Helixi63 – 664Combined sources
Beta strandi70 – 778Combined sources
Beta strandi81 – 833Combined sources
Beta strandi86 – 9813Combined sources
Beta strandi100 – 1045Combined sources
Beta strandi124 – 13310Combined sources
Beta strandi139 – 1457Combined sources
Helixi146 – 15914Combined sources
Helixi164 – 1674Combined sources
Beta strandi170 – 1723Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP68826.
SMRiP68826. Positions 1-183.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP68826.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

P68826-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA
60 70 80 90 100
KRYGLRSGVG LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV
110 120 130 140 150
QEAYLPTGEG CLSVDDNVAG LVHRHNRITI KAKDIEGNDI QLRLKGYPAI
160 170 180
VFQHEIDHLN GVMFYDHIDK NHPLQPHTDA VEV
Length:183
Mass (Da):20,559
Last modified:December 21, 2004 - v1
Checksum:i32A64066A6FEAB0E
GO

Mass spectrometryi

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY007227 Genomic DNA. Translation: AAG02249.1.
RefSeqiWP_000957037.1. NZ_JYFP01000005.1.

Genome annotation databases

KEGGisaud:CH52_00430.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY007227 Genomic DNA. Translation: AAG02249.1.
RefSeqiWP_000957037.1. NZ_JYFP01000005.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP68826.
SMRiP68826. Positions 1-183.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL1100.

Chemistry

BindingDBiP68826.
ChEMBLiCHEMBL2010635.

Proteomic databases

PRIDEiP68826.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGisaud:CH52_00430.

Phylogenomic databases

eggNOGiCOG0242.

Enzyme and pathway databases

BRENDAi3.5.1.88. 3352.

Miscellaneous databases

EvolutionaryTraceiP68826.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

  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).

Entry informationi

Entry nameiDEF_STAAU
AccessioniPrimary (citable) accession number: P68826
Secondary accession number(s): Q9F4L4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: December 21, 2004
Last modified: July 22, 2015
This is version 57 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.