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Protein

Peptide deformylase

Gene

def

Organism
Finegoldia magna (strain ATCC 29328) (Peptostreptococcus magnus)
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 bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule 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

BioCyciFMAG334413:GJ6M-709-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:FMG_0661
OrganismiFinegoldia magna (strain ATCC 29328) (Peptostreptococcus magnus)
Taxonomic identifieri334413 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptoniphilaceaeFinegoldia
ProteomesiUP000001319 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 162162Peptide deformylasePRO_1000097311Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi334413.FMG_0661.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiCFCHELD.
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.

B0S139-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALRQIRLEN DPILRKKSRE VEKIDDRIKQ IVEDMFETMY ENKGIGLACV
60 70 80 90 100
QVGMLKRIVV IDMQDEDGKM VLINPKIIEK SEEKQINIEG CLSVPGKNGY
110 120 130 140 150
VERPKTVVVE YTDLNGNTQR VMGTDYKAHC FCHELDHLDG VLYTDKVLNL
160
SEEEVERLNN EK
Length:162
Mass (Da):18,712
Last modified:April 8, 2008 - v1
Checksum:iB0B4BE5B6D4E5842
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008971 Genomic DNA. Translation: BAG08079.1.
RefSeqiYP_001691969.1. NC_010376.1.

Genome annotation databases

EnsemblBacteriaiBAG08079; BAG08079; FMG_0661.
KEGGifma:FMG_0661.
PATRICi21886993. VBIFinMag33027_0866.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008971 Genomic DNA. Translation: BAG08079.1.
RefSeqiYP_001691969.1. NC_010376.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi334413.FMG_0661.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAG08079; BAG08079; FMG_0661.
KEGGifma:FMG_0661.
PATRICi21886993. VBIFinMag33027_0866.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiCFCHELD.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciFMAG334413:GJ6M-709-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 Finegoldia magna, an anaerobic opportunistic pathogen."
    Goto T., Yamashita A., Hirakawa H., Matsutani M., Todo K., Ohshima K., Toh H., Miyamoto K., Kuhara S., Hattori M., Shimizu T., Akimoto S.
    DNA Res. 15:39-47(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 29328.

Entry informationi

Entry nameiDEF_FINM2
AccessioniPrimary (citable) accession number: B0S139
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: April 1, 2015
This is version 48 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.