Reviewed, UniProtKB/Swiss-Prot A6L7J9 (DEF_BACV8)

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:	BVU_4061

Organism

Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / NCTC 11154) [Complete proteome] [HAMAP]

Taxonomic identifier

435590 [NCBI]

Taxonomic lineage

Bacteria › Bacteroidetes › Bacteroidia › Bacteroidales › Bacteroidaceae › Bacteroides

Protein attributes

Sequence length	184 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 – 184	184	Peptide deformylase HAMAP MF_00163		PRO_0000301005
Sites
	Active site	141	1	By similarity
	Metal binding	98	1	Iron By similarity
	Metal binding	140	1	Iron By similarity
	Metal binding	144	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	A6L7J9-1 [UniParc]. Last modified July 24, 2007. Version 1. Checksum: B9E1607904FC722B	FASTA	184	21,019
	10 20 30 40 50 60 MILPIYVYGQ PVLRKEAEDI TPDYPNLKEL IANMFETMNR ADGVGLAAPQ IGLPIRVVTI 70 80 90 100 110 120 DLDVMSDDLP EFKDFRRAYI NPHILEVGGE EVSMEEGCLS LPGIHEAVKR PDRIHVTYLD 130 140 150 160 170 180 EELKEHDEWV EGYLARVMQH EFDHLDGKMF IDHLSALRKQ MIKGKLGAML KGKARCSYKV KTIK

References

[1]

"Evolution of symbiotic bacteria in the distal human intestine." Xu J., Mahowald M.A., Ley R.E., Lozupone C.A., Hamady M., Martens E.C., Henrissat B., Coutinho P.M., Minx P., Latreille P., Cordum H., Van Brunt A., Kim K., Fulton R.S., Fulton L.A., Clifton S.W., Wilson R.K., Knight R.D., Gordon J.I. PLoS Biol. 5:1574-1586(2007) [PubMed: 17579514] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000139 Genomic DNA. Translation: ABR41663.1.
RefSeq	YP_001301285.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	A6L7J9.
Genome annotation databases
GeneID	5305020.
GenomeReviews	Gene locus BVU_4061 in contig CP000139_GR.
KEGG	bvu:BVU_4061.
NMPDR	fig|435590.6.peg.3775.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	KELIANM.
Family and domain databases
HAMAP	MF_00163. [Tree]
InterPro	IPR000181. Fmet_deformylase. [Graphical view]
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

DEF_BACV8

Accession

Primary (citable) accession number: A6L7J9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	July 24, 2007
Last modified:	November 3, 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)