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Protein

Peptide deformylase

Gene

def

Organism
Thermus thermophilus
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 (By similarity).By similarity

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi102IronBy similarity1
Metal bindingi145IronBy similarity1
Active sitei146By similarity1
Metal bindingi149IronBy similarity1

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 deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
OrganismiThermus thermophilus
Taxonomic identifieri274 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828671 – 192Peptide deformylaseAdd BLAST192

Interactioni

Protein-protein interaction databases

STRINGi262724.TTC1662.

Structurei

Secondary structure

1192
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi11 – 14Combined sources4
Helixi26 – 39Combined sources14
Beta strandi43 – 46Combined sources4
Helixi47 – 50Combined sources4
Beta strandi54 – 60Combined sources7
Turni75 – 77Combined sources3
Beta strandi81 – 93Combined sources13
Beta strandi96 – 100Combined sources5
Beta strandi110 – 115Combined sources6
Beta strandi117 – 124Combined sources8
Beta strandi130 – 136Combined sources7
Helixi137 – 150Combined sources14
Helixi155 – 158Combined sources4
Helixi161 – 170Combined sources10
Helixi172 – 181Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1V3YX-ray1.81A/B1-192[»]
ProteinModelPortaliP43522.
SMRiP43522.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP43522.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.

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.

P43522-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVYPIRLYGD PVLRRKARPV EDFSGIKRLA EDMLETMFEA KGVGLAAPQI
60 70 80 90 100
GLSQRLFVAV EYADEPEGEE ERPLRELVRR VYVVANPVIT YREGLVEGTE
110 120 130 140 150
GCLSLPGLYS EEVPRAERIR VEYQDEEGRG RVLELEGYMA RVFQHEIDHL
160 170 180 190
DGILFFERLP KPKREAFLEA NRAELVRFQK EARALLKELS QG
Length:192
Mass (Da):22,092
Last modified:November 1, 1995 - v1
Checksum:i665945183A251361
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X79087 Genomic DNA. Translation: CAA55695.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X79087 Genomic DNA. Translation: CAA55695.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1V3YX-ray1.81A/B1-192[»]
ProteinModelPortaliP43522.
SMRiP43522.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi262724.TTC1662.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.

Miscellaneous databases

EvolutionaryTraceiP43522.

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_THETH
AccessioniPrimary (citable) accession number: P43522
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: November 2, 2016
This is version 84 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

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.