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Protein

Peptide deformylase

Gene

def

Organism
Mycobacterium gilvum (strain PYR-GCK) (Mycobacterium flavescens (strain ATCC 700033 / PYR-GCK))
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

BioCyciMGIL350054:GHK8-175-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:Mflv_0175
OrganismiMycobacterium gilvum (strain PYR-GCK) (Mycobacterium flavescens (strain ATCC 700033 / PYR-GCK))
Taxonomic identifieri350054 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000000232: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 197197Peptide deformylasePRO_1000076946Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi350054.Mflv_0175.

Structurei

3D structure databases

ProteinModelPortaliA4T2T4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiEHMLGSA.
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.

A4T2T4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAVRPICIVG DPVLHTATEP IPVGPDGSLP ADLADLITDL YDTMDAAHGV
60 70 80 90 100
GLAANQIGVN KRVFVYDCAD ARKKTVRRRG VVVNPVLETS EVPETMPDPE
110 120 130 140 150
DDDEGCLSVP GESFPTGRAD WARVTGLDAD GTPITIEGTD LFARMLQHET
160 170 180 190
GHLDGFLYLD SLIGRNARAA KRAVKSHGWG VPGLTWMPGE DPDPFGH
Length:197
Mass (Da):21,093
Last modified:May 15, 2007 - v1
Checksum:i908F6FEE8C925A78
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000656 Genomic DNA. Translation: ABP42670.1.
RefSeqiWP_011891177.1. NC_009338.1.
YP_001131458.1. NC_009338.1.

Genome annotation databases

EnsemblBacteriaiABP42670; ABP42670; Mflv_0175.
GeneIDi4971797.
KEGGimgi:Mflv_0175.
PATRICi18028332. VBIMycGil17082_0180.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000656 Genomic DNA. Translation: ABP42670.1.
RefSeqiWP_011891177.1. NC_009338.1.
YP_001131458.1. NC_009338.1.

3D structure databases

ProteinModelPortaliA4T2T4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi350054.Mflv_0175.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP42670; ABP42670; Mflv_0175.
GeneIDi4971797.
KEGGimgi:Mflv_0175.
PATRICi18028332. VBIMycGil17082_0180.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiEHMLGSA.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciMGIL350054:GHK8-175-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PYR-GCK.

Entry informationi

Entry nameiDEF_MYCGI
AccessioniPrimary (citable) accession number: A4T2T4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: May 15, 2007
Last modified: February 4, 2015
This is version 57 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.