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Protein

Peptide deformylase

Gene

def

Organism
Streptococcus agalactiae serotype III (strain NEM316)
Status
Reviewed-Annotation score: Annotation score: 2 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 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:gbs1883
OrganismiStreptococcus agalactiae serotype III (strain NEM316)
Taxonomic identifieri211110 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000000823 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828471 – 204Peptide deformylaseAdd BLAST204

Interactioni

Protein-protein interaction databases

STRINGi211110.gbs1883.

Structurei

Secondary structure

1204
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 8Combined sources6
Helixi16 – 18Combined sources3
Helixi25 – 28Combined sources4
Helixi40 – 57Combined sources18
Helixi59 – 65Combined sources7
Beta strandi70 – 74Combined sources5
Helixi75 – 78Combined sources4
Beta strandi82 – 90Combined sources9
Beta strandi101 – 118Combined sources18
Beta strandi120 – 125Combined sources6
Beta strandi144 – 153Combined sources10
Beta strandi159 – 164Combined sources6
Helixi166 – 179Combined sources14
Helixi184 – 187Combined sources4
Beta strandi201 – 203Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5JEXX-ray2.00A1-204[»]
5JEYX-ray2.80A1-204[»]
5JEZX-ray1.70A1-204[»]
5JF0X-ray1.60A1-204[»]
5JF1X-ray2.00A1-204[»]
5JF2X-ray2.00A1-204[»]
5JF3X-ray1.60A1-204[»]
5JF4X-ray2.40A1-204[»]
5JF5X-ray1.80A1-204[»]
5JF6X-ray1.70A1-204[»]
5JF7X-ray2.10A1-204[»]
5JF8X-ray1.80A1-204[»]
ProteinModelPortaliQ8E378.
SMRiQ8E378.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107YB9. 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.
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.

Q8E378-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAIDKLVKA SHLIDMNDII REGNPTLRKV AEEVTFPLSE KEEILGEKMM
60 70 80 90 100
QFLKHSQDPI MAEKLGLRGG VGLAAPQLDI SKRIIAVLVP NVEDAQGNPP
110 120 130 140 150
KEAYSLQEVM YNPKVVSHSV QDAALSDGEG CLSVDREVPG YVVRHARVTI
160 170 180 190 200
EYFDKTGEKH RLKLKGYNSI VVQHEIDHID GIMFYDRINE KNPFAVKEGL

LILE
Length:204
Mass (Da):22,830
Last modified:March 1, 2003 - v1
Checksum:i50097F6CCF8524EF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL766854 Genomic DNA. Translation: CAD47542.1.
RefSeqiWP_001272875.1. NC_004368.1.

Genome annotation databases

EnsemblBacteriaiCAD47542; CAD47542; CAD47542.
KEGGisan:gbs1883.
PATRICi19639689. VBIStrAga3577_1930.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL766854 Genomic DNA. Translation: CAD47542.1.
RefSeqiWP_001272875.1. NC_004368.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5JEXX-ray2.00A1-204[»]
5JEYX-ray2.80A1-204[»]
5JEZX-ray1.70A1-204[»]
5JF0X-ray1.60A1-204[»]
5JF1X-ray2.00A1-204[»]
5JF2X-ray2.00A1-204[»]
5JF3X-ray1.60A1-204[»]
5JF4X-ray2.40A1-204[»]
5JF5X-ray1.80A1-204[»]
5JF6X-ray1.70A1-204[»]
5JF7X-ray2.10A1-204[»]
5JF8X-ray1.80A1-204[»]
ProteinModelPortaliQ8E378.
SMRiQ8E378.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi211110.gbs1883.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAD47542; CAD47542; CAD47542.
KEGGisan:gbs1883.
PATRICi19639689. VBIStrAga3577_1930.

Phylogenomic databases

eggNOGiENOG4107YB9. 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.
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.
ProtoNetiSearch...

Entry informationi

Entry nameiDEF_STRA3
AccessioniPrimary (citable) accession number: Q8E378
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: March 1, 2003
Last modified: March 15, 2017
This is version 85 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

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.