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Protein

Peptide deformylase

Gene

def

Organism
Desulfitobacterium hafniense (strain Y51)
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 bindingi88 – 881IronUniRule annotation
Metal bindingi130 – 1301IronUniRule annotation
Active sitei131 – 1311UniRule annotation
Metal bindingi134 – 1341IronUniRule 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

BioCyciDHAF138119:GHT5-2758-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:DSY2694
OrganismiDesulfitobacterium hafniense (strain Y51)
Taxonomic identifieri138119 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptococcaceaeDesulfitobacterium
ProteomesiUP000001946 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 150150Peptide deformylasePRO_0000301025Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi138119.DSY2694.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
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.

Q24U09-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIYQIVEIG SEVLREKAVP VKEITPNIEK LLDNMLDTLY DANGVGLAAP
60 70 80 90 100
QVGVSKRVVV IDVGEGPIEL INPVIIAKEG EDLDDEGCLS IPGITGQVAR
110 120 130 140 150
AAKVKVEALN RQGELQVIEG EGLLARCLQH EIDHLEGILF VDKAKKTQRR
Length:150
Mass (Da):16,272
Last modified:April 18, 2006 - v1
Checksum:i39F668C27CEA6BB8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008230 Genomic DNA. Translation: BAE84483.1.
RefSeqiYP_518927.1. NC_007907.1.

Genome annotation databases

EnsemblBacteriaiBAE84483; BAE84483; DSY2694.
KEGGidsy:DSY2694.
PATRICi21674160. VBIDesHaf65307_3015.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008230 Genomic DNA. Translation: BAE84483.1.
RefSeqiYP_518927.1. NC_007907.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi138119.DSY2694.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAE84483; BAE84483; DSY2694.
KEGGidsy:DSY2694.
PATRICi21674160. VBIDesHaf65307_3015.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciDHAF138119:GHT5-2758-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 the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195."
    Nonaka H., Keresztes G., Shinoda Y., Ikenaga Y., Abe M., Naito K., Inatomi K., Furukawa K., Inui M., Yukawa H.
    J. Bacteriol. 188:2262-2274(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Y51.

Entry informationi

Entry nameiDEF_DESHY
AccessioniPrimary (citable) accession number: Q24U09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: April 18, 2006
Last modified: April 29, 2015
This is version 63 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.