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Protein

Peptide deformylase

Gene

def

Organism
Mycobacterium abscessus (strain ATCC 19977 / DSM 44196)
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 bindingi106 – 1061IronUniRule annotation
Metal bindingi148 – 1481IronUniRule annotation
Active sitei149 – 1491UniRule annotation
Metal bindingi152 – 1521IronUniRule 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

BioCyciMABS36809-WGS:GSQO-4206-MONOMER.
MABS561007:GJTG-4206-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:MAB_4187
OrganismiMycobacterium abscessus (strain ATCC 19977 / DSM 44196)
Taxonomic identifieri561007 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium abscessus
ProteomesiUP000007137 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 197197Peptide deformylasePRO_1000097324Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi561007.MAB_4187.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
OMAiICARVIL.
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.

B1MIN9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIVPIRIVG DPVLHTPTQP VPVGPDGSLP DDLPELIANM YETMDAANGV
60 70 80 90 100
GLAANQIGVP LRLFVYDCAE TRGGGTRHRG VVINPVLETS EIPETMPDPD
110 120 130 140 150
DDEEGCLSVP GESFPTGRAG WARVTGLDAD GKEVTLEGND LFARMLQHET
160 170 180 190
GHLDGFLYID KLIGRNARAA KRAVKSNGWG VPGLSWTPGQ VADPFGH
Length:197
Mass (Da):20,958
Last modified:April 29, 2008 - v1
Checksum:i2476DE2AF572897D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU458896 Genomic DNA. Translation: CAM64260.1.

Genome annotation databases

EnsemblBacteriaiCAM64260; CAM64260; MAB_4187.
PATRICi17980200. VBIMycAbs55940_4265.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU458896 Genomic DNA. Translation: CAM64260.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi561007.MAB_4187.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAM64260; CAM64260; MAB_4187.
PATRICi17980200. VBIMycAbs55940_4265.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
OMAiICARVIL.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciMABS36809-WGS:GSQO-4206-MONOMER.
MABS561007:GJTG-4206-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. "Acquisition of foreign virulence genes by the cystic fibrosis pathogen Mycobacterium abscessus."
    Genoscope
    Ripoll F., Pasek S., Schenowitz C., Dossat C., Barbe V., Rottman M., Heym B., Herrmann J.L., Daffe M., Brosch R., Risler J.L., Gaillard J.L.
    Submitted (FEB-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19977 / DSM 44196.

Entry informationi

Entry nameiDEF_MYCA9
AccessioniPrimary (citable) accession number: B1MIN9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: April 1, 2015
This is version 52 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.