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Protein

Peptide deformylase

Gene

def

Organism
Treponema pallidum subsp. pallidum (strain SS14)
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 bindingi86 – 861IronUniRule annotation
Metal bindingi128 – 1281IronUniRule annotation
Active sitei129 – 1291UniRule annotation
Metal bindingi132 – 1321IronUniRule 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

BioCyciTPAL455434:GJ9E-797-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:TPASS_0757
OrganismiTreponema pallidum subsp. pallidum (strain SS14)
Taxonomic identifieri455434 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesSpirochaetaceaeTreponema
ProteomesiUP000001202: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 162162Peptide deformylasePRO_1000097357Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi455434.TPASS_0757.

Structurei

3D structure databases

ProteinModelPortaliB2S3Z6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIRSAEWY.
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.

B2S3Z6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELKFLGEPC LTTVSEPVSE VDEQLRAFIS GMFRVMRGAG GVGLAAPQVG
60 70 80 90 100
RTVRVFVVDV EHHVRAFINP QITAASEEQS SYEEGCLSIP HIYERVLRPR
110 120 130 140 150
RVSVQYLDEN GKRCAVDADG ILARVIQHEY DHLDGILFLD RIDEKRRDDA
160
LRRYAALRGT IR
Length:162
Mass (Da):18,323
Last modified:July 1, 2008 - v1
Checksum:i15AEA6C940819CC1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000805 Genomic DNA. Translation: ACD71175.1.
RefSeqiYP_001933754.1. NC_010741.1.
YP_008119484.1. NC_021508.1.

Genome annotation databases

EnsemblBacteriaiACD71175; ACD71175; TPASS_0757.
GeneIDi15843620.
6333575.
KEGGitpp:TPASS_0757.
PATRICi20529299. VBITrePal10923_0800.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000805 Genomic DNA. Translation: ACD71175.1.
RefSeqiYP_001933754.1. NC_010741.1.
YP_008119484.1. NC_021508.1.

3D structure databases

ProteinModelPortaliB2S3Z6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi455434.TPASS_0757.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD71175; ACD71175; TPASS_0757.
GeneIDi15843620.
6333575.
KEGGitpp:TPASS_0757.
PATRICi20529299. VBITrePal10923_0800.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIRSAEWY.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciTPAL455434:GJ9E-797-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. "Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays."
    Matejkova P., Strouhal M., Smajs D., Norris S.J., Palzkill T., Petrosino J.F., Sodergren E., Norton J.E., Singh J., Richmond T.A., Molla M.N., Albert T.J., Weinstock G.M.
    BMC Microbiol. 8:76-76(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SS14.

Entry informationi

Entry nameiDEF_TREPS
AccessioniPrimary (citable) accession number: B2S3Z6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 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.