Q89BN9 (DEF_BRAJA) 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:	bll8109

Organism

Bradyrhizobium japonicum

Taxonomic identifier

375 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

Protein attributes

Sequence length	174 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 MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP MF_00163
Cofactor	Binds 1 Fe2+ ion By similarity. HAMAP MF_00163
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 Reference proteome
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 174	174	Peptide deformylase HAMAP MF_00163		PRO_0000082751
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)
	Q89BN9 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: C4D96157F6D26558	FASTA	174	19,930
	10 20 30 40 50 60 MALREIIILP DKQLRLVSKP IEKVTTEIRK LADDMFETMY DAPGIGLAAI QIAQPLRLIT 70 80 90 100 110 120 MDLAKRDENG ETKPEPRVFI NPEVIASSEE LSVYEEGCLS IPEYYEEVER PAKVRVRFTD 130 140 150 160 170 LDGKVHEEDA EGLYATCIQH EIDHLNGVLF VDYLSKLKRD RVLKKFEKAA KRAE

References

[1]

"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110." Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S. DNA Res. 9:189-197(2002) [PubMed: 12597275] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: USDA 110.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000040 Genomic DNA. Translation: BAC53374.1.
RefSeq	NP_774749.1. NC_004463.1.
3D structure databases
ProteinModelPortal	Q89BN9.
SMR	Q89BN9. Positions 2-172.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1049081.
GenomeReviews	Gene locus bll8109 in contig BA000040_GR.
KEGG	bja:bll8109.
NMPDR	fig|224911.1.peg.8109.
PATRIC	21200236. VBIBraJap65052_8344.
Phylogenomic databases
HOGENOM	HBG665227.
OMA	GVLFVDY.
PhylomeDB	Q89BN9.
ProtClustDB	PRK00150.
Enzyme and pathway databases
BioCyc	BJAP224911:BLL8109-MONOMER.
Family and domain databases
HAMAP	MF_00163. Pep_deformylase. [Tree]
InterPro	IPR000181. Fmet_deformylase. IPR023635. Peptide_deformylase. [Graphical view]
Gene3D	G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
KO	K01462.
PANTHER	PTHR10458. Fmet_deformylase. 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_BRAJA

Accession

Primary (citable) accession number: Q89BN9

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	January 25, 2012
This is version 50 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program