Reviewed, UniProtKB/Swiss-Prot A1A2Z1 (DEF_BIFAA)

Names and origin

Protein names

Recommended name:
    Peptide deformylase
      Short name=PDF
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase

Gene names

Name:	def
Ordered Locus Names:	BAD_1293

Organism

Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083) [Complete proteome] [HAMAP]

Taxonomic identifier

367928 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Bifidobacteriales › Bifidobacteriaceae › Bifidobacterium

Protein attributes

Sequence length	218 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	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.
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP MF_00163
Cofactor	Binds 1 Fe2+ ion By similarity.
Sequence similarities	Belongs to the polypeptide deformylase family.

Ontologies

Keywords
Biological process	Protein biosynthesis
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: HAMAP
Molecular function	iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW peptide deformylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 218	218	Peptide deformylase HAMAP MF_00163		PRO_0000301010
Sites
	Active site	173	1	By similarity
	Metal binding	130	1	Iron By similarity
	Metal binding	172	1	Iron By similarity
	Metal binding	176	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1A2Z1-1 [UniParc]. Last modified January 23, 2007. Version 1. Checksum: 4CE4C976E83FFDCE	FASTA	218	24,536
	10 20 30 40 50 60 MFGHNSKVDL ELNREVEKLI KTGGKEKIMP IVQAGEPVLR QQTIAYDGQL SRKTLDKLID 70 80 90 100 110 120 TMRTTMLEAP GVGLAATQIG LGLALAVVED HVCEGDDGDP REAAEFPFHA IINPSYEPIG 130 140 150 160 170 180 TETRSFYEGC LSFDGYQAVR KRWLDITARW QDEDGNKHEE HLHGWPARIF QHETDHLSGE 190 200 210 LYIDQAEIRS LTTNENLEDF WCEDPVPTEA AAELGFEL

References

[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].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AP009256 Genomic DNA. Translation: BAF40074.1.
RefSeq	YP_910156.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	4556246.
GenomeReviews	Gene locus BAD_1293 in contig AP009256_GR.
KEGG	bad:BAD_1293.
NMPDR	fig|1680.3.peg.923.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	A1A2Z1. GWPARIL.
Family and domain databases
HAMAP	MF_00163. [Tree]
InterPro	IPR000181. Fmet_deformylase. [Graphical view]
Gene3D	G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
PANTHER	PTHR10458. Fmet_deformylase. 1 hit.
Pfam	PF01327. Pep_deformylase. 1 hit. [Graphical view]
PIRSF	PIRSF004749. Pep_def. 1 hit.
PRINTS	PR01576. PDEFORMYLASE.
ProDom	PD003844. Fmet_deformylase. 1 hit. [Graphical view] [Entries sharing at least one domain]
ProtoNet	Search...

Entry information

Entry name

DEF_BIFAA

Accession

Primary (citable) accession number: A1A2Z1

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 16 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)