Reviewed, UniProtKB/Swiss-Prot A1AGH8 (DEF_ECOK1)

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:	Ecok1_32740
ORF Names:	APECO1_3160

Organism

Escherichia coli O1:K1 / APEC [Complete proteome] [HAMAP]

Taxonomic identifier

405955 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	169 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 – 169	169	Peptide deformylase HAMAP MF_00163		PRO_0000301031
Sites
	Active site	134	1	By similarity
	Metal binding	91	1	Iron By similarity
	Metal binding	133	1	Iron By similarity
	Metal binding	137	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1AGH8-1 [UniParc]. Last modified January 23, 2007. Version 1. Checksum: C485EB6C1D2D91B8	FASTA	169	19,328
	10 20 30 40 50 60 MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV 70 80 90 100 110 120 IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE 130 140 150 160 LEADGLLAIC IQHEMDHLVG KLFMDYLSPL KQQRIRQKVE KLDRLKARA

References

[1]

"The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes." Johnson T.J., Kariyawasam S., Wannemuehler Y., Mangiamele P., Johnson S.J., Doetkott C., Skyberg J.A., Lynne A.M., Johnson J.R., Nolan L.K. J. Bacteriol. 189:3228-3236(2007) [PubMed: 17293413] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000468 Genomic DNA. Translation: ABJ02768.1.
RefSeq	YP_858892.1.
3D structure databases
SMR	A1AGH8. Positions 2-169.
ModBase	Search...
Genome annotation databases
GeneID	4491717.
GenomeReviews	Gene locus Ecok1_32740 in contig CP000468_GR.
KEGG	ecv:APECO1_3160.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	A1AGH8. IGVPRRM.
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]
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...
Other Resources
BindingDB	A1AGH8.

Entry information

Entry name

DEF_ECOK1

Accession

Primary (citable) accession number: A1AGH8

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 18 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)