Reviewed, UniProtKB/Swiss-Prot Q825U9 (DEF3_STRAW)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 3
      Short name=PDF 3
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase 3

Gene names

Name:	def3
Ordered Locus Names:	SAV_7349

Organism

Streptomyces avermitilis [Complete proteome] [HAMAP]

Taxonomic identifier

33903 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Streptomycineae › Streptomycetaceae › Streptomyces

Protein attributes

Sequence length	224 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 – 224	224	Peptide deformylase 3 HAMAP MF_00163		PRO_0000082851
Sites
	Active site	178	1	By similarity
	Metal binding	135	1	Iron By similarity
	Metal binding	177	1	Iron By similarity
	Metal binding	181	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q825U9-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: D0ED0E6FB0806A23	FASTA	224	23,892
	10 20 30 40 50 60 MASESDRTVP DTRSASRPLA DRVEELLATG GPLPIVAAGD PVLRRGAEPY DGQLGPGLLA 70 80 90 100 110 120 RFVEALRLTM HAAPGVGLAA PQVGVGLRIA VIEDPAPVPE EVGAVRGRVP QPFRVLVNPS 130 140 150 160 170 180 YEAVGSDRAA FFEGCLSVPG WQAVVARPAR VRLTALDEHG RAVDEEFTGW PARIVQHETD 190 200 210 220 HLDGMLYLDR AELRSLSSNE AMALRWSQPT PERAAAALGF ALPD

References

[1]

"Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites." Omura S., Ikeda H., Ishikawa J., Hanamoto A., Takahashi C., Shinose M., Takahashi Y., Horikawa H., Nakazawa H., Osonoe T., Kikuchi H., Shiba T., Sakaki Y., Hattori M. Proc. Natl. Acad. Sci. U.S.A. 98:12215-12220(2001) [PubMed: 11572948] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165.

[2]

"Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis." Ikeda H., Ishikawa J., Hanamoto A., Shinose M., Kikuchi H., Shiba T., Sakaki Y., Hattori M., Omura S. Nat. Biotechnol. 21:526-531(2003) [PubMed: 12692562] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165.

Cross-references

Sequence databases
EMBLGenBankDDBJ	BA000030 Genomic DNA. Translation: BAC75060.1.
RefSeq	NP_828525.1.
3D structure databases
HSSP	HSSP built from PDB template 1N5N based on UniProtKB Q9I7A8.
ModBase	Search...
Genome annotation databases
GeneID	1211719.
GenomeReviews	Gene locus SAV_7349 in contig BA000030_GR.
KEGG	sma:SAV_7349.
NMPDR	fig|227882.1.peg.7351.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q825U9.
OMA	GWQARIV.
Enzyme and pathway databases
BioCyc	SAVE227882:SAV7349-MON.
BRENDA	3.5.1.88. 140873.
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

DEF3_STRAW

Accession

Primary (citable) accession number: Q825U9

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	November 3, 2009
This is version 39 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)