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Protein

Peptide deformylase

Gene

def

Organism
Orientia tsutsugamushi (strain Ikeda) (Rickettsia tsutsugamushi)
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciOTSU334380:GC7O-1356-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:OTT_1330
OrganismiOrientia tsutsugamushi (strain Ikeda) (Rickettsia tsutsugamushi)
Taxonomic identifieri334380 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeOrientia
ProteomesiUP000001033 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 181181Peptide deformylasePRO_1000097329Add
BLAST

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiSLFVMCV.
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.

B3CTU1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSILSLITAP DPILKKVASP VDTVNDSIRQ LMDDMLETMY HNHGVGLAAP
60 70 80 90 100
QVAVSKRIIV LDLSKVDIKE DNITNSEYKY PLFMVNPIVK AISNQTATAK
110 120 130 140 150
EGCLSLPKQA IEVSRYHEIQ VTYLDYYNKL TTLNAEGWLA RAIQHEVDHL
160 170 180
DGILLVDYLS NLKKEAALNT LSKIKDAAYD K
Length:181
Mass (Da):20,228
Last modified:July 22, 2008 - v1
Checksum:i15BC0478026416B1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008981 Genomic DNA. Translation: BAG40788.1.
RefSeqiWP_012461836.1. NC_010793.1.

Genome annotation databases

EnsemblBacteriaiBAG40788; BAG40788; OTT_1330.
KEGGiott:OTT_1330.
PATRICi22828964. VBIOriTsu129072_1496.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008981 Genomic DNA. Translation: BAG40788.1.
RefSeqiWP_012461836.1. NC_010793.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAG40788; BAG40788; OTT_1330.
KEGGiott:OTT_1330.
PATRICi22828964. VBIOriTsu129072_1496.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiSLFVMCV.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciOTSU334380:GC7O-1356-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. "The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution."
    Nakayama K., Yamashita A., Kurokawa K., Morimoto T., Ogawa M., Fukuhara M., Urakami H., Ohnishi M., Uchiyama I., Ogura Y., Ooka T., Oshima K., Tamura A., Hattori M., Hayashi T.
    DNA Res. 15:185-199(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Ikeda.

Entry informationi

Entry nameiDEF_ORITI
AccessioniPrimary (citable) accession number: B3CTU1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 22, 2008
Last modified: July 22, 2015
This is version 53 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.