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Protein

Peptide deformylase 1

Gene

def1

Organism
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
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 bindingi90IronUniRule annotation1
Metal bindingi132IronUniRule annotation1
Active sitei133UniRule annotation1
Metal bindingi136IronUniRule 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 deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
Ordered Locus Names:BC_3865
OrganismiBacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Taxonomic identifieri226900 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillusBacillus cereus group
Proteomesi
  • UP000001417 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000827351 – 156Peptide deformylase 1Add BLAST156

Proteomic databases

PRIDEiQ819U0.

Interactioni

Protein-protein interaction databases

STRINGi226900.BC3865.

Structurei

Secondary structure

1156
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi12 – 15Combined sources4
Helixi26 – 41Combined sources16
Beta strandi45 – 48Combined sources4
Helixi49 – 52Combined sources4
Beta strandi56 – 62Combined sources7
Turni65 – 67Combined sources3
Beta strandi69 – 88Combined sources20
Beta strandi98 – 111Combined sources14
Beta strandi117 – 123Combined sources7
Helixi124 – 137Combined sources14
Helixi142 – 144Combined sources3
Beta strandi146 – 149Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WS0X-ray1.70A1-156[»]
1WS1X-ray2.00A1-156[»]
ProteinModelPortaliQ819U0.
SMRiQ819U0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ819U0.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242. LUCA.
KOiK01462.
OMAiMYREGCL.

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.

Q819U0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVLEIIKHP NEVLETPCER VINFDKKLVK LLKDMHETML IADGVGLAAP
60 70 80 90 100
QVGVSLQVAV VDVDDDTGKI ELINPSILEK RGEQVGPEGC LSFPGLYGEV
110 120 130 140 150
ERADYIKVRA QNRRGKVFLL EAEGFLARAI QHEIDHLHGV LFTSKVTRYY

EENELE
Length:156
Mass (Da):17,480
Last modified:June 1, 2003 - v1
Checksum:i0B68AB39485C4D8A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016877 Genomic DNA. Translation: AAP10787.1.
RefSeqiNP_833586.1. NC_004722.1.
WP_000279455.1. NC_004722.1.

Genome annotation databases

EnsemblBacteriaiAAP10787; AAP10787; BC_3865.
GeneIDi1206210.
KEGGibce:BC3865.
PATRICi32603761. VBIBacCer54481_3984.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016877 Genomic DNA. Translation: AAP10787.1.
RefSeqiNP_833586.1. NC_004722.1.
WP_000279455.1. NC_004722.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WS0X-ray1.70A1-156[»]
1WS1X-ray2.00A1-156[»]
ProteinModelPortaliQ819U0.
SMRiQ819U0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi226900.BC3865.

Proteomic databases

PRIDEiQ819U0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAP10787; AAP10787; BC_3865.
GeneIDi1206210.
KEGGibce:BC3865.
PATRICi32603761. VBIBacCer54481_3984.

Phylogenomic databases

eggNOGiCOG0242. LUCA.
KOiK01462.
OMAiMYREGCL.

Miscellaneous databases

EvolutionaryTraceiQ819U0.

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 nameiDEF1_BACCR
AccessioniPrimary (citable) accession number: Q819U0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: November 2, 2016
This is version 92 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.