P63914 (DEF_BRUSU) Reviewed, UniProtKB/Swiss-Prot

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:	BRA1035, BS1330_II1027

Organism

Brucella suis biovar 1 (strain 1330) [Complete proteome] [HAMAP]

Taxonomic identifier

204722 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Brucellaceae › Brucella › Brucella suis

Protein attributes

Sequence length	175 AA.
Sequence status	Complete.
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. HAMAP-Rule MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163
Cofactor	Binds 1 Fe2+ ion By similarity. HAMAP-Rule MF_00163
Sequence similarities	Belongs to the polypeptide deformylase family.
Sequence caution	The sequence AAN34202.1 differs from that shown. Reason: Erroneous initiation. The sequence AEM20479.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

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: InterPro 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 – 175	175	Peptide deformylase HAMAP-Rule MF_00163		PRO_0000082753
Sites
	Active site	137	1	By similarity
	Metal binding	94	1	Iron By similarity
	Metal binding	136	1	Iron By similarity
	Metal binding	140	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	P63914 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 873A6ABCF3EFFCE2	FASTA	175	19,660
	10 20 30 40 50 60 MSVKPLIILP DPVLRQVSKP VERFDDQLRK FASDMFDTMY DAPGIGLAAI QVGEPIRMLV 70 80 90 100 110 120 IDLAKEGEPK APHIFVNPTI VQSSDKRSTY EEGCLSIPDY YAEVERPATV KVNYFDADGK 130 140 150 160 170 PQSMEADGLM ATCLQHEIDH LNGVLFIDHI SKLKRDMVIK KFKKLASQRA SKKVL

References

[1]

"The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts." Paulsen I.T., Seshadri R., Nelson K.E., Eisen J.A., Heidelberg J.F., Read T.D., Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C., DeBoy R.T., Durkin A.S., Kolonay J.F., Madupu R., Nelson W.C., Ayodeji B., Kraul M. , Shetty J., Malek J.A., Van Aken S.E., Riedmuller S., Tettelin H., Gill S.R., White O., Salzberg S.L., Hoover D.L., Lindler L.E., Halling S.M., Boyle S.M., Fraser C.M. Proc. Natl. Acad. Sci. U.S.A. 99:13148-13153(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 1330.

[2]

"Revised genome sequence of Brucella suis 1330." Tae H., Shallom S., Settlage R., Preston D., Adams L.G., Garner H.R. J. Bacteriol. 193:6410-6410(2011) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 1330.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE014292 Genomic DNA. Translation: AAN34202.1. Different initiation. CP002998 Genomic DNA. Translation: AEM20479.1. Different initiation.
RefSeq	NP_700197.1. NC_004311.2. YP_005614705.1. NC_017250.1.
3D structure databases
ProteinModelPortal	P63914.
ModBase	Search...
Protein-protein interaction databases
STRING	204722.BRA1035.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAN34202; AAN34202; BRA1035. AEM20479; AEM20479; BS1330_II1027.
GeneID	1165480. 12139260.
KEGG	bms:BRA1035. bsi:BS1330_II1027.
PATRIC	17794905. VBIBruSui107850_3260.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HOG000243509.
KO	K01462.
ProtClustDB	PRK00150.
Family and domain databases
Gene3D	3.90.45.10. 1 hit.
HAMAP	MF_00163. Pep_deformylase.
InterPro	IPR000181. Fmet_deformylase. IPR023635. Peptide_deformylase. [Graphical view]
PANTHER	PTHR10458. PTHR10458. 1 hit.
Pfam	PF01327. Pep_deformylase. 1 hit. [Graphical view]
PIRSF	PIRSF004749. Pep_def. 1 hit.
PRINTS	PR01576. PDEFORMYLASE.
SUPFAM	SSF56420. Fmet_deformylase. 1 hit.
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DEF_BRUSU

Accession

Primary (citable) accession number: P63914
Secondary accession number(s): G0KE41, Q8YDB4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 1, 2013
This is version 52 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program