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Protein

Peptide deformylase

Gene

def

Organism
Staphylococcus aureus (strain COL)
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 bindingi111IronUniRule annotation1
Metal bindingi154IronUniRule annotation1
Active sitei155UniRule annotation1
Metal bindingi158IronUniRule 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
Synonyms:def1, pdf1
Ordered Locus Names:SACOL1100
OrganismiStaphylococcus aureus (strain COL)
Taxonomic identifieri93062 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus
Proteomesi
  • UP000000530 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828381 – 183Peptide deformylaseAdd BLAST183

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL1100

Structurei

Secondary structure

1183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 6Combined sources3
Helixi13 – 16Combined sources4
Helixi28 – 44Combined sources17
Helixi47 – 52Combined sources6
Beta strandi59 – 62Combined sources4
Helixi63 – 66Combined sources4
Beta strandi70 – 77Combined sources8
Beta strandi81 – 83Combined sources3
Beta strandi86 – 98Combined sources13
Beta strandi100 – 104Combined sources5
Beta strandi124 – 133Combined sources10
Beta strandi139 – 146Combined sources8
Helixi147 – 159Combined sources13
Helixi164 – 167Combined sources4
Beta strandi170 – 172Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3U7KX-ray1.90A1-183[»]
3U7LX-ray2.01A1-183[»]
3U7MX-ray2.15A1-183[»]
3U7NX-ray2.30A1-183[»]
ProteinModelPortaliQ5HGZ3
SMRiQ5HGZ3
ModBaseiSearch...
MobiDBiSearch...

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.

Q5HGZ3-1 [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 DHPLQPHTDA VEV
Length:183
Mass (Da):20,560
Last modified:February 15, 2005 - v1
Checksum:i32A64066AE5CAB0E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000046 Genomic DNA Translation: AAW37980.1
RefSeqiWP_000957036.1, NC_002951.2

Genome annotation databases

EnsemblBacteriaiAAW37980; AAW37980; SACOL1100
KEGGisac:SACOL1100

Similar proteinsi

Entry informationi

Entry nameiDEF_STAAC
AccessioniPrimary (citable) accession number: Q5HGZ3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: February 15, 2005
Last modified: March 28, 2018
This is version 79 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
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Main funding by: National Institutes of Health