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Protein

Peptide deformylase

Gene

def

Organism
Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)
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 bindingi130 – 1301IronUniRule annotation
Metal bindingi172 – 1721IronUniRule annotation
Active sitei173 – 1731UniRule annotation
Metal bindingi176 – 1761IronUniRule 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

BioCyciBADO367928:GHPT-1349-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:BAD_1293
OrganismiBifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)
Taxonomic identifieri367928 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeBifidobacterialesBifidobacteriaceaeBifidobacterium
ProteomesiUP000008702 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 218218Peptide deformylasePRO_0000301010Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi367928.BAD_1293.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiTFTNIHW.
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]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.

Sequencei

Sequence statusi: Complete.

A1A2Z1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFGHNSKVDL ELNREVEKLI KTGGKEKIMP IVQAGEPVLR QQTIAYDGQL
60 70 80 90 100
SRKTLDKLID TMRTTMLEAP GVGLAATQIG LGLALAVVED HVCEGDDGDP
110 120 130 140 150
REAAEFPFHA IINPSYEPIG TETRSFYEGC LSFDGYQAVR KRWLDITARW
160 170 180 190 200
QDEDGNKHEE HLHGWPARIF QHETDHLSGE LYIDQAEIRS LTTNENLEDF
210
WCEDPVPTEA AAELGFEL
Length:218
Mass (Da):24,536
Last modified:January 23, 2007 - v1
Checksum:i4CE4C976E83FFDCE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009256 Genomic DNA. Translation: BAF40074.1.
RefSeqiYP_910156.1. NC_008618.1.

Genome annotation databases

EnsemblBacteriaiBAF40074; BAF40074; BAD_1293.
KEGGibad:BAD_1293.
PATRICi21102031. VBIBifAdo27973_1370.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009256 Genomic DNA. Translation: BAF40074.1.
RefSeqiYP_910156.1. NC_008618.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi367928.BAD_1293.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF40074; BAF40074; BAD_1293.
KEGGibad:BAD_1293.
PATRICi21102031. VBIBifAdo27973_1370.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiTFTNIHW.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciBADO367928:GHPT-1349-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]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Bifidobacterium adolescentis complete genome sequence."
    Suzuki T., Tsuda Y., Kanou N., Inoue T., Kumazaki K., Nagano S., Hirai S., Tanaka K., Watanabe K.
    Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a.

Entry informationi

Entry nameiDEF_BIFAA
AccessioniPrimary (citable) accession number: A1A2Z1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: January 23, 2007
Last modified: April 1, 2015
This is version 51 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.