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Protein

Peptide deformylase

Gene

def

Organism
Streptococcus pyogenes serotype M3 (strain SSI-1)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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.UniRule annotation

Catalytic activityi

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

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi131 – 1311IronUniRule annotation
Metal bindingi174 – 1741IronUniRule annotation
Active sitei175 – 1751UniRule annotation
Metal bindingi178 – 1781IronUniRule annotation

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

BioCyciSPYO193567:GHDO-1751-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:SPs1686
OrganismiStreptococcus pyogenes serotype M3 (strain SSI-1)
Taxonomic identifieri193567 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 204204Peptide deformylasePRO_0000411436Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliP0DC97.
SMRiP0DC97. Positions 2-204.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000243507.
KOiK01462.
OMAiQDPVMGE.
OrthoDBiEOG6PZXGQ.

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.

P0DC97-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAQDKLIKP SHLITMDDII REGNPTLRAV AKEVSLPLCD EDILLGEKMM
60 70 80 90 100
QFLKHSQDPV MAEKLGLRAG VGLAAPQIDV SKRIIAVLVP NLPDKEGNPP
110 120 130 140 150
KEAYSWQEVL YNPKIVSHSV QDAALSDGEG CLSVDRVVEG YVVRHARVTV
160 170 180 190 200
DYYDKEGQQH RIKLKGYNAI VVQHEIDHIN GVLFYDRINA KNPFETKEEL

LILD
Length:204
Mass (Da):22,862
Last modified:July 27, 2011 - v1
Checksum:i89F8EDE94D94DC05
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000034 Genomic DNA. Translation: BAC64781.1.
RefSeqiNP_802948.1. NC_004606.1.
WP_002982624.1. NC_004606.1.

Genome annotation databases

EnsemblBacteriaiBAC64781; BAC64781; BAC64781.
KEGGisps:SPs1686.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000034 Genomic DNA. Translation: BAC64781.1.
RefSeqiNP_802948.1. NC_004606.1.
WP_002982624.1. NC_004606.1.

3D structure databases

ProteinModelPortaliP0DC97.
SMRiP0DC97. Positions 2-204.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC64781; BAC64781; BAC64781.
KEGGisps:SPs1686.

Phylogenomic databases

HOGENOMiHOG000243507.
KOiK01462.
OMAiQDPVMGE.
OrthoDBiEOG6PZXGQ.

Enzyme and pathway databases

BioCyciSPYO193567:GHDO-1751-MONOMER.

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. "Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution."
    Nakagawa I., Kurokawa K., Yamashita A., Nakata M., Tomiyasu Y., Okahashi N., Kawabata S., Yamazaki K., Shiba T., Yasunaga T., Hayashi H., Hattori M., Hamada S.
    Genome Res. 13:1042-1055(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SSI-1.

Entry informationi

Entry nameiDEF_STRPQ
AccessioniPrimary (citable) accession number: P0DC97
Secondary accession number(s): P68772, P82590, Q99XY7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 27, 2011
Last sequence update: July 27, 2011
Last modified: June 24, 2015
This is version 25 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. 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.