Reviewed, UniProtKB/Swiss-Prot Q886I1 (DEF2_PSESM)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 2
      Short name=PDF 2
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase 2

Gene names

Name:	def2
Ordered Locus Names:	PSPTO_1598

Organism

Pseudomonas syringae pv. tomato [Complete proteome] [HAMAP]

Taxonomic identifier

323 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas

Protein attributes

Sequence length	179 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 – 179	179	Peptide deformylase 2 HAMAP MF_00163		PRO_0000082823
Sites
	Active site	144	1	By similarity
	Metal binding	101	1	Iron By similarity
	Metal binding	143	1	Iron By similarity
	Metal binding	147	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q886I1-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 7CD70D0ACA744A98	FASTA	179	20,051
	10 20 30 40 50 60 MIRNILKMGD ERLLRIAPPV PAEMFGSSEL ETLIADMFET MHSVGGVGLA APQIGIDLQL 70 80 90 100 110 120 VIFGFERSER YPQAEAVPQT ILLNPLITPL HPGVEEGWEG CLSVPGLRGM VDRYQSIRYE 130 140 150 160 170 GFDPDGQPIE RIAHGFHARV VQHECDHLIG RLYPSRITDF SKFGFMDVMF PDMDPNADE

References

[1]

"The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000." Buell C.R., Joardar V., Lindeberg M., Selengut J., Paulsen I.T., Gwinn M.L., Dodson R.J., DeBoy R.T., Durkin A.S., Kolonay J.F., Madupu R., Daugherty S.C., Brinkac L.M., Beanan M.J., Haft D.H., Nelson W.C., Davidsen T.M., Zafar N. , Zhou L., Liu J., Yuan Q., Khouri H.M., Fedorova N.B., Tran B., Russell D., Berry K.J., Utterback T.R., Van Aken S.E., Feldblyum T.V., D'Ascenzo M., Deng W.-L., Ramos A.R., Alfano J.R., Cartinhour S., Chatterjee A.K., Delaney T.P., Lazarowitz S.G., Martin G.B., Schneider D.J., Tang X., Bender C.L., White O., Fraser C.M., Collmer A. Proc. Natl. Acad. Sci. U.S.A. 100:10181-10186(2003) [PubMed: 12928499] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: DC3000.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE016853 Genomic DNA. Translation: AAO55118.1.
RefSeq	NP_791423.1.
3D structure databases
HSSP	HSSP built from PDB template 1N5N based on UniProtKB Q9I7A8.
ModBase	Search...
Genome annotation databases
GeneID	1183235.
GenomeReviews	Gene locus PSPTO_1598 in contig AE016853_GR.
KEGG	pst:PSPTO_1598.
NMPDR	fig|223283.1.peg.1561.
TIGR	PSPTO_1598.
Phylogenomic databases
HOGENOM	Q886I1.
OMA	LYPSRIT.
Enzyme and pathway databases
BioCyc	PSYR223283:PSPTO_1598-MON.
BRENDA	3.5.1.88. 289554.
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

DEF2_PSESM

Accession

Primary (citable) accession number: Q886I1

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2003
Last sequence update:	June 1, 2003
Last modified:	November 3, 2009
This is version 45 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)