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Protein

Peptide deformylase

Gene

def

Organism
Staphylococcus aureus (strain COL)
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.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

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, 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.
OMAiQDPVMGE.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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.

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.
GeneIDi28381359.
KEGGisac:SACOL1100.
PATRICi19528440. VBIStaAur112458_1073.

Cross-referencesi

Sequence databases

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

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...

Protein-protein interaction databases

STRINGi93062.SACOL1100.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAW37980; AAW37980; SACOL1100.
GeneIDi28381359.
KEGGisac:SACOL1100.
PATRICi19528440. VBIStaAur112458_1073.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243507.
KOiK01462.
OMAiQDPVMGE.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

Entry informationi

Entry nameiDEF_STAAC
AccessioniPrimary (citable) accession number: Q5HGZ3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: February 15, 2005
Last modified: November 2, 2016
This is version 74 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, Complete proteome

Documents

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

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 one 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.