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B0U4M4

- DEF_XYLFM

UniProt

B0U4M4 - DEF_XYLFM

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Protein
Peptide deformylase
Gene
def, Xfasm12_1929
Organism
Xylella fastidiosa (strain M12)
Status
Reviewed - 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 By similarity.UniRule annotation

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Binds 1 Fe2+ ion By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi94 – 941Iron By similarity
Metal bindingi136 – 1361Iron By similarity
Active sitei137 – 1371 By similarity
Metal bindingi140 – 1401Iron By similarity

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 deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
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 deformylaseUniRule annotation
PRO_1000097362Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi405440.Xfasm12_1929.

Structurei

3D structure databases

ProteinModelPortaliB0U4M4.
SMRiB0U4M4. Positions 1-168.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEETGEEW.
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

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MALLPILEFP DPRLRTKAVR VGVAEVVSSS FQTLLDDMFE TMYAAPGIGL    50
AATQVNVHQR FMVVDVSEEK NAPMVFINPE IVTREGDQVF QEGCLSVPGI 100
HADVTRALSI VVRFLDRHGD EQQLTAEGLL AVCIQHEMDH LDGKLFIDYL 150
SPLKRDMVRR KLEKQRRRAS 170
Length:170
Mass (Da):19,158
Last modified:April 8, 2008 - v1
Checksum:iF2CD729A4C733A5C
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
CP000941 Genomic DNA. Translation: ACA12803.1 .
RefSeqi YP_001776433.1. NC_010513.1.

3D structure databases

ProteinModelPortali B0U4M4.
SMRi B0U4M4. Positions 1-168.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 405440.Xfasm12_1929.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACA12803 ; ACA12803 ; Xfasm12_1929 .
GeneIDi 6120209.
KEGGi xfm:Xfasm12_1929.
PATRICi 24140646. VBIXylFas124301_2265.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
KOi K01462.
OMAi EETGEEW.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci XFAS405440:GH0D-1969-MONOMER.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PIRSFi PIRSF004749. Pep_def. 1 hit.
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

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: May 14, 2014
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

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