Q88B43 (DEF1_PSESM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptide deformylase 1
Short name=PDF 1
EC=3.5.1.88

Alternative name(s):
Polypeptide deformylase 1

Gene names

Name:	def1
Ordered Locus Names:	PSPTO_0177

Organism

Pseudomonas syringae pv. tomato (strain DC3000) [Complete proteome] [HAMAP]

Taxonomic identifier

223283 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas

Protein attributes

Sequence length	168 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
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 – 168	168	Peptide deformylase 1 HAMAP MF_00163		PRO_0000082822
Sites
	Active site	135	1	By similarity
	Metal binding	92	1	Iron By similarity
	Metal binding	134	1	Iron By similarity
	Metal binding	138	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q88B43 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 04BA118A2ABF0B69	FASTA	168	19,185
	10 20 30 40 50 60 MAILNILEFP DSRLRTLAKP VAMVDDGIRQ LVDDMFETMY EAPGIGLAAT QVNVHKRVVV 70 80 90 100 110 120 MDLSEDRSAP MVFINPEIEK LTDEMDQYQE GCLSVPGFYE NVDRPQKVRV KALDRDGKPY 130 140 150 160 ELVAEGLLAI CIQHECDHLN GKLFVDYLSN LKRDRIKKKL EKQHKLNA

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
EMBL GenBank DDBJ	AE016853 Genomic DNA. Translation: AAO53731.1.
RefSeq	NP_790036.1. NC_004578.1.
3D structure databases
ProteinModelPortal	Q88B43.
SMR	Q88B43. Positions 1-165.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1181785.
GenomeReviews	Gene locus PSPTO_0177 in contig AE016853_GR.
KEGG	pst:PSPTO_0177.
NMPDR	fig|223283.1.peg.174.
PATRIC	19991506. VBIPseSyr93040_0183.
TIGR	PSPTO_0177.
Phylogenomic databases
HOGENOM	HBG665227.
OMA	GVLFVDY.
ProtClustDB	PRK00150.
Enzyme and pathway databases
BioCyc	PSYR223283:PSPTO_0177-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

DEF1_PSESM

Accession

Primary (citable) accession number: Q88B43

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2003
Last sequence update:	June 1, 2003
Last modified:	January 25, 2012
This is version 60 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program