A4YLB9 (DEF_BRASO) 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:	BRADO0770

Organism

Bradyrhizobium sp. (strain ORS278) [Complete proteome] [HAMAP]

Taxonomic identifier

114615 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

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.
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: 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_0000301013
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)
	A4YLB9 [UniParc]. Last modified May 29, 2007. Version 1. Checksum: 49B0C8291E41D5C7	FASTA	175	19,976
	10 20 30 40 50 60 MSLREIIILP DRQLRLVSKP VEKVTPEIRQ LVDDMFQTMY DAPGIGLAAI QVAQPLRVIT 70 80 90 100 110 120 MDLAKPDSGG ETKREPRVFI NPEIIAKSDE LSVYEEGCLS IPEYYEEVER PARVRVRFTD 130 140 150 160 170 LDGVVREEDA EGLYATCIQH EIDHLNGVLF IDYLSKLKRD RVMKKFTKAA KRAGE

References

[1]

"Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia." Giraud E., Moulin L., Vallenet D., Barbe V., Cytryn E., Avarre J.-C., Jaubert M., Simon D., Cartieaux F., Prin Y., Bena G., Hannibal L., Fardoux J., Kojadinovic M., Vuillet L., Lajus A., Cruveiller S., Rouy Z. , Mangenot S., Segurens B., Dossat C., Franck W.L., Chang W.-S., Saunders E., Bruce D., Richardson P., Normand P., Dreyfus B., Pignol D., Stacey G., Emerich D., Vermeglio A., Medigue C., Sadowsky M. Science 316:1307-1312(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ORS278.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CU234118 Genomic DNA. Translation: CAL74695.1.
RefSeq	YP_001202933.1. NC_009445.1.
3D structure databases
ProteinModelPortal	A4YLB9.
SMR	A4YLB9. Positions 2-172.
ModBase	Search...
Protein-protein interaction databases
STRING	114615.BRADO0770.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	CAL74695; CAL74695; BRADO0770.
GeneID	5115231.
KEGG	bra:BRADO0770.
PATRIC	21217803. VBIBraSp122330_0731.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HOG000243509.
KO	K01462.
OMA	EMDQYQE.
ProtClustDB	PRK00150.
Enzyme and pathway databases
BioCyc	BSP114615:GJN5-731-MONOMER.
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_BRASO

Accession

Primary (citable) accession number: A4YLB9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	May 29, 2007
Last modified:	May 1, 2013
This is version 38 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program