Reviewed, UniProtKB/Swiss-Prot Q8EKQ8 (DEF1_SHEON)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 1
      Short name=PDF 1
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase 1

Gene names

Name:	def1
Ordered Locus Names:	SO_0032

Organism

Shewanella oneidensis [Complete proteome] [HAMAP]

Taxonomic identifier

70863 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Alteromonadales › Shewanellaceae › Shewanella

Protein attributes

Sequence length	168 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 – 168	168	Peptide deformylase 1 HAMAP MF_00163		PRO_0000082834
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)
	Q8EKQ8-1 [UniParc]. Last modified March 1, 2003. Version 1. Checksum: 6B069474CA908488	FASTA	168	19,247
	10 20 30 40 50 60 MALLKVLRFP DERLRTQATP ITEFNAELQT QIDDMFETMY QEKGIGLAAT QVDYHKQLIV 70 80 90 100 110 120 MDLQDEVERP KVFINPEIIA SSGDFCNEEG CLSVPGIYAK VDRAEFVTVK ALDRHGNEFT 130 140 150 160 VEADDLFAIC IQHEMDHLKG KLFVDYLSPL KRQRIKQKLE KAAKQDAK

References

[1]

"Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis." Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C., Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A., Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C., DeBoy R.T. , Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R., Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J., Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J., Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V., Smith H.O., Venter J.C., Nealson K.H., Fraser C.M. Nat. Biotechnol. 20:1118-1123(2002) [PubMed: 12368813] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: MR-1.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE014299 Genomic DNA. Translation: AAN53119.1.
RefSeq	NP_715674.1.
3D structure databases
HSSP	HSSP built from PDB template 1LRU based on UniProtKB P27251.
ModBase	Search...
Genome annotation databases
GeneID	1167930.
GenomeReviews	Gene locus SO_0032 in contig AE014299_GR.
KEGG	son:SO_0032.
NMPDR	fig|211586.1.peg.32.
TIGR	SO_0032.
Phylogenomic databases
HOGENOM	Q8EKQ8.
OMA	CIQHECD.
Enzyme and pathway databases
BioCyc	SONE211586:SO_0032-MON.
BRENDA	3.5.1.88. 257422.
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...

Entry information

Entry name

DEF1_SHEON

Accession

Primary (citable) accession number: Q8EKQ8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2003
Last sequence update:	March 1, 2003
Last modified:	November 3, 2009
This is version 41 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)