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Protein

Peptide deformylase

Gene

def

Organism
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
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 bindingi130IronUniRule annotation1
Metal bindingi173IronUniRule annotation1
Active sitei174UniRule annotation1
Metal bindingi177IronUniRule 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
Ordered Locus Names:spr1310
OrganismiStreptococcus pneumoniae (strain ATCC BAA-255 / R6)
Taxonomic identifieri171101 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000000586 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828581 – 203Peptide deformylaseAdd BLAST203

Interactioni

Protein-protein interaction databases

STRINGi171101.spr1310.

Chemistry databases

BindingDBiQ8DP79.

Structurei

Secondary structure

1203
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 strandi103 – 117Combined sources15
Beta strandi119 – 124Combined sources6
Beta strandi143 – 152Combined sources10
Beta strandi158 – 163Combined sources6
Helixi165 – 178Combined sources14
Helixi183 – 186Combined sources4
Beta strandi189 – 191Combined sources3
Beta strandi199 – 202Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AI7X-ray2.00A1-202[»]
2AIAX-ray1.70A1-202[»]
2AIEX-ray1.70P1-202[»]
3SVJX-ray1.55P1-203[»]
4EOXX-ray1.78P1-203[»]
ProteinModelPortaliQ8DP79.
SMRiQ8DP79.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8DP79.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107YB9. 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.

Q8DP79-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAIERITKA AHLIDMNDII REGNPTLRTV AEEVTFPLSD QEIILGEKMM
60 70 80 90 100
QFLKHSQDPV MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ
110 120 130 140 150
EAYDLEAIMY NPKIVSHSVQ DAALGEGEGC LSVDRNVPGY VVRHARVTVD
160 170 180 190 200
YFDKDGEKHR IKLKGYNSIV VQHEIDHING IMFYDRINEK DPFAVKDGLL

ILE
Length:203
Mass (Da):22,692
Last modified:March 1, 2003 - v1
Checksum:iE332956982A67161
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007317 Genomic DNA. Translation: AAL00114.1.
PIRiE98035.
RefSeqiNP_358903.1. NC_003098.1.
WP_001272961.1. NC_003098.1.

Genome annotation databases

EnsemblBacteriaiAAL00114; AAL00114; spr1310.
GeneIDi934523.
KEGGispr:spr1310.
PATRICi19702614. VBIStrPne107296_1422.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007317 Genomic DNA. Translation: AAL00114.1.
PIRiE98035.
RefSeqiNP_358903.1. NC_003098.1.
WP_001272961.1. NC_003098.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AI7X-ray2.00A1-202[»]
2AIAX-ray1.70A1-202[»]
2AIEX-ray1.70P1-202[»]
3SVJX-ray1.55P1-203[»]
4EOXX-ray1.78P1-203[»]
ProteinModelPortaliQ8DP79.
SMRiQ8DP79.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi171101.spr1310.

Chemistry databases

BindingDBiQ8DP79.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL00114; AAL00114; spr1310.
GeneIDi934523.
KEGGispr:spr1310.
PATRICi19702614. VBIStrPne107296_1422.

Phylogenomic databases

eggNOGiENOG4107YB9. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243507.
KOiK01462.
OMAiQDPVMGE.

Miscellaneous databases

EvolutionaryTraceiQ8DP79.
PROiQ8DP79.

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_STRR6
AccessioniPrimary (citable) accession number: Q8DP79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: March 1, 2003
Last modified: November 2, 2016
This is version 99 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, Reference 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.