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Protein

Peptide deformylase

Gene

def

Organism
Orientia tsutsugamushi (strain Boryong) (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

  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

BioCyciOTSU357244:GCA5-1881-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:OTBS_1849
OrganismiOrientia tsutsugamushi (strain Boryong) (Rickettsia tsutsugamushi)
Taxonomic identifieri357244 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeOrientia
ProteomesiUP000001565: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 181181Peptide deformylasePRO_0000301072Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi357244.OTBS_1849.

Structurei

3D structure databases

ProteinModelPortaliA5CF65.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
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.

A5CF65-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSILSLVTAP DPILKKVSSP VDTVNDSIRQ LIDDMLETMY HNHGVGLAAP
60 70 80 90 100
QVAVSKRIIV LDLSKVDIEE DNITNSEYKY PLFMVNPIVK AISNQTVTAK
110 120 130 140 150
EGCLSLPKQA IEVSRYHEIQ VTYLDYYNKL KTLNAAGWLA RAIQHEVDHL
160 170 180
DGILLVDYLS NLKKEATLNT LSKIKDAAYD K
Length:181
Mass (Da):20,240
Last modified:June 12, 2007 - v1
Checksum:i6826C003DB7FCDD9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM494475 Genomic DNA. Translation: CAM80944.1.
RefSeqiWP_011945081.1. NC_009488.1.
YP_001249099.1. NC_009488.1.

Genome annotation databases

EnsemblBacteriaiCAM80944; CAM80944; OTBS_1849.
GeneIDi5218231.
KEGGiots:OTBS_1849.
PATRICi22825176. VBIOriTsu83812_1997.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM494475 Genomic DNA. Translation: CAM80944.1.
RefSeqiWP_011945081.1. NC_009488.1.
YP_001249099.1. NC_009488.1.

3D structure databases

ProteinModelPortaliA5CF65.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi357244.OTBS_1849.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAM80944; CAM80944; OTBS_1849.
GeneIDi5218231.
KEGGiots:OTBS_1849.
PATRICi22825176. VBIOriTsu83812_1997.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciOTSU357244:GCA5-1881-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 Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes."
    Cho N.-H., Kim H.-R., Lee J.-H., Kim S.-Y., Kim J., Cha S., Kim S.-Y., Darby A.C., Fuxelius H.-H., Yin J., Kim J.H., Kim J., Lee S.J., Koh Y.-S., Jang W.-J., Park K.-H., Andersson S.G.E., Choi M.-S., Kim I.-S.
    Proc. Natl. Acad. Sci. U.S.A. 104:7981-7986(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Boryong.

Entry informationi

Entry nameiDEF_ORITB
AccessioniPrimary (citable) accession number: A5CF65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: June 12, 2007
Last modified: March 4, 2015
This is version 51 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

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.