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Protein

Peptide deformylase

Gene

def

Organism
Xylella fastidiosa (strain M12)
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 bindingi94 – 941IronUniRule annotation
Metal bindingi136 – 1361IronUniRule annotation
Active sitei137 – 1371UniRule annotation
Metal bindingi140 – 1401IronUniRule 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

BioCyciXFAS405440:GH0D-1969-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:Xfasm12_1929
OrganismiXylella fastidiosa (strain M12)
Taxonomic identifieri405440 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000008539: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylasePRO_1000097362Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi405440.Xfasm12_1929.

Structurei

3D structure databases

ProteinModelPortaliB0U4M4.
SMRiB0U4M4. Positions 1-168.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
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.

B0U4M4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MALLPILEFP DPRLRTKAVR VGVAEVVSSS FQTLLDDMFE TMYAAPGIGL
60 70 80 90 100
AATQVNVHQR FMVVDVSEEK NAPMVFINPE IVTREGDQVF QEGCLSVPGI
110 120 130 140 150
HADVTRALSI VVRFLDRHGD EQQLTAEGLL AVCIQHEMDH LDGKLFIDYL
160 170
SPLKRDMVRR KLEKQRRRAS
Length:170
Mass (Da):19,158
Last modified:April 8, 2008 - v1
Checksum:iF2CD729A4C733A5C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000941 Genomic DNA. Translation: ACA12803.1.
RefSeqiYP_001776433.1. NC_010513.1.

Genome annotation databases

EnsemblBacteriaiACA12803; ACA12803; Xfasm12_1929.
GeneIDi6120209.
KEGGixfm:Xfasm12_1929.
PATRICi24140646. VBIXylFas124301_2265.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000941 Genomic DNA. Translation: ACA12803.1.
RefSeqiYP_001776433.1. NC_010513.1.

3D structure databases

ProteinModelPortaliB0U4M4.
SMRiB0U4M4. Positions 1-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi405440.Xfasm12_1929.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA12803; ACA12803; Xfasm12_1929.
GeneIDi6120209.
KEGGixfm:Xfasm12_1929.
PATRICi24140646. VBIXylFas124301_2265.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiIEYYDEN.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciXFAS405440:GH0D-1969-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. "Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California."
    Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E.L.
    J. Bacteriol. 192:4534-4534(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: M12.

Entry informationi

Entry nameiDEF_XYLFM
AccessioniPrimary (citable) accession number: B0U4M4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: January 7, 2015
This is version 47 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.