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Protein

Peptide deformylase

Gene

def

Organism
Bacillus clausii (strain KSM-K16)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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 bindingi110IronUniRule annotation1
Metal bindingi153IronUniRule annotation1
Active sitei154UniRule annotation1
Metal bindingi157IronUniRule 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:ABC2423
OrganismiBacillus clausii (strain KSM-K16)
Taxonomic identifieri66692 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001168 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003010021 – 183Peptide deformylaseAdd BLAST183

Interactioni

Protein-protein interaction databases

STRINGi66692.ABC2423.

Structurei

3D structure databases

ProteinModelPortaliQ5WFA2.
SMRiQ5WFA2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243507.
KOiK01462.
OMAiMILMKDI.
OrthoDBiPOG091H02B0.

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.

Q5WFA2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITMDDIVRE GNPILRKVAE PVELPLTDED KQTLVDMLEF IKNSQDPEIA
60 70 80 90 100
EKYGLRPGVG LAAPQIGISK RLFAIHATDE NGNLYSMGIA NPKVVSHSVE
110 120 130 140 150
TNELENGEGC LSVDRDVPGL VPRRARLTIT GVDHEGNDVR MRLRGYIAIV
160 170 180
FQHELDHLDG IMFYDRIEGL EDPFKKPLPG FAL
Length:183
Mass (Da):20,388
Last modified:November 23, 2004 - v1
Checksum:i8A3009F0269B3B8F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006627 Genomic DNA. Translation: BAD64958.1.
RefSeqiWP_011247266.1. NC_006582.1.

Genome annotation databases

EnsemblBacteriaiBAD64958; BAD64958; ABC2423.
KEGGibcl:ABC2423.
PATRICi18924442. VBIBacCla58185_2584.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006627 Genomic DNA. Translation: BAD64958.1.
RefSeqiWP_011247266.1. NC_006582.1.

3D structure databases

ProteinModelPortaliQ5WFA2.
SMRiQ5WFA2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi66692.ABC2423.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD64958; BAD64958; ABC2423.
KEGGibcl:ABC2423.
PATRICi18924442. VBIBacCla58185_2584.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
HOGENOMiHOG000243507.
KOiK01462.
OMAiMILMKDI.
OrthoDBiPOG091H02B0.

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_BACSK
AccessioniPrimary (citable) accession number: Q5WFA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: November 23, 2004
Last modified: November 2, 2016
This is version 78 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

Complete proteome, Reference proteome

Documents

  1. 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.