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Protein

Peptide deformylase

Gene

def

Organism
Streptococcus pyogenes serotype M1
Status
Reviewed-Annotation score: -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.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)DescriptionActionsGraphical viewLength
Metal bindingi131IronUniRule annotation1
Metal bindingi174IronUniRule annotation1
Active sitei175UniRule annotation1
Metal bindingi178IronUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding

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:SPy_1958, M5005_Spy1669
OrganismiStreptococcus pyogenes serotype M1
Taxonomic identifieri301447 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000000750 Componenti: Chromosome

Pathology & Biotechi

Chemistry databases

DrugBankiDB04310 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828591 – 204Peptide deformylaseAdd BLAST204

Proteomic databases

PaxDbiP68771
PRIDEiP68771

Interactioni

Protein-protein interaction databases

STRINGi160490.SPy_1958

Structurei

Secondary structure

1204
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 7Combined sources5
Helixi16 – 18Combined sources3
Helixi25 – 28Combined sources4
Helixi40 – 56Combined sources17
Helixi59 – 65Combined sources7
Beta strandi71 – 74Combined sources4
Helixi75 – 78Combined sources4
Beta strandi82 – 90Combined sources9
Beta strandi101 – 118Combined sources18
Beta strandi120 – 125Combined sources6
Beta strandi144 – 153Combined sources10
Beta strandi159 – 164Combined sources6
Helixi166 – 178Combined sources13
Turni179 – 181Combined sources3
Helixi184 – 187Combined sources4
Beta strandi200 – 203Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OS3X-ray2.26A2-204[»]
ProteinModelPortaliP68771
SMRiP68771
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP68771

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
HOGENOMiHOG000243507
KOiK01462
OMAiMILMKDI

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
PIRSFiPIRSF004749 Pep_def, 1 hit
PRINTSiPR01576 PDEFORMYLASE
SUPFAMiSSF56420 SSF56420, 1 hit
TIGRFAMsiTIGR00079 pept_deformyl, 1 hit

Sequencei

Sequence statusi: Complete.

P68771-1 [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:December 21, 2004 - v1
Checksum:i89F8EDE94D94DC05
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004092 Genomic DNA Translation: AAK34651.1
CP000017 Genomic DNA Translation: AAZ52287.1
RefSeqiNP_269930.1, NC_002737.2

Genome annotation databases

EnsemblBacteriaiAAK34651; AAK34651; SPy_1958
AAZ52287; AAZ52287; M5005_Spy1669
GeneIDi901633
KEGGispy:SPy_1958
spz:M5005_Spy1669
PATRICifig|160490.10.peg.1705

Similar proteinsi

Entry informationi

Entry nameiDEF_STRP1
AccessioniPrimary (citable) accession number: P68771
Secondary accession number(s): P82590, Q48WI8, Q99XY7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: December 21, 2004
Last modified: March 28, 2018
This is version 88 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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