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Protein

Peptide deformylase

Gene

def

Organism
Leptospira biflexa serovar Patoc (strain Patoc 1 / Ames)
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi103 – 1031IronUniRule annotation
Metal bindingi145 – 1451IronUniRule annotation
Active sitei146 – 1461UniRule annotation
Metal bindingi149 – 1491IronUniRule annotation

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciLBIF355278:GHTJ-1519-MONOMER.

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:LBF_1521
OrganismiLeptospira biflexa serovar Patoc (strain Patoc 1 / Ames)
Taxonomic identifieri355278 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesLeptospiraceaeLeptospira
ProteomesiUP000001846: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 179179Peptide deformylasePRO_1000097321Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi355278.LBF_1521.

Structurei

3D structure databases

ProteinModelPortaliB0SHH1.
SMRiB0SHH1. Positions 2-179.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. 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.

B0SHH1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAVRKILKIG NPILRQTSED VSESEIQTKD FKKLIRDMFE TMRHADGVGL
60 70 80 90 100
AAPQIGVLKK LVVVGQEDDN ERYPGTPEVP NQIILNPEIT PLSPPRDGFW
110 120 130 140 150
EGCLSVPGMR GYVERPNKIR MKWRDENYVE HDEIIEGYRA IVLQHECDHL
160 170
FGVLYVDRLK STKLFGYNED IDTAGKLLD
Length:179
Mass (Da):20,479
Last modified:April 8, 2008 - v1
Checksum:i50A5293F6C91CCE5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000777 Genomic DNA. Translation: ABZ94032.1.
RefSeqiWP_012388559.1. NC_010842.1.
YP_001962610.1. NC_010842.1.

Genome annotation databases

EnsemblBacteriaiABZ94032; ABZ94032; LBF_1521.
GeneIDi6388120.
KEGGilbf:LBF_1521.
PATRICi22342115. VBILepBif95142_1617.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000777 Genomic DNA. Translation: ABZ94032.1.
RefSeqiWP_012388559.1. NC_010842.1.
YP_001962610.1. NC_010842.1.

3D structure databases

ProteinModelPortaliB0SHH1.
SMRiB0SHH1. Positions 2-179.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi355278.LBF_1521.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABZ94032; ABZ94032; LBF_1521.
GeneIDi6388120.
KEGGilbf:LBF_1521.
PATRICi22342115. VBILepBif95142_1617.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciLBIF355278:GHTJ-1519-MONOMER.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. 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...

Publicationsi

  1. "Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis."
    Picardeau M., Bulach D.M., Bouchier C., Zuerner R.L., Zidane N., Wilson P.J., Creno S., Kuczek E.S., Bommezzadri S., Davis J.C., McGrath A., Johnson M.J., Boursaux-Eude C., Seemann T., Rouy Z., Coppel R.L., Rood J.I., Lajus A.
    , Davies J.K., Medigue C., Adler B.
    PLoS ONE 3:E1607-E1607(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Patoc 1 / Ames.

Entry informationi

Entry nameiDEF_LEPBA
AccessioniPrimary (citable) accession number: B0SHH1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: January 7, 2015
This is version 44 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.