Q88RR1 (DEF1_PSEPK) 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:	PP_0068

Organism

Pseudomonas putida (strain KT2440) [Complete proteome] [HAMAP]

Taxonomic identifier

160488 [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_0000082820
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)
	Q88RR1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 8E550C63A77F0130	FASTA	168	19,410
	10 20 30 40 50 60 MAILNILEFP DPRLRTLAKP VTEFDDALRQ LIDDMFETMY EAPGIGLAAT QVNVHKQVVV 70 80 90 100 110 120 MDLSEDRSEP RVFINPSVEE LTHDMGQYQE GCLSVPGFYE NVDRPLRVRV KAQDRDGKPF 130 140 150 160 ELECEGLLAV CVQHEFDHLN GKLFVDYLSQ LKRDRIKKKL EKQHRQQA

References

[1]

"Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440." Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M., Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F., Madupu R., Nelson W.C., White O. , Peterson J.D., Khouri H.M., Hance I., Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A., Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M. Environ. Microbiol. 4:799-808(2002) [PubMed: 12534463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: KT2440.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE015451 Genomic DNA. Translation: AAN65702.1.
RefSeq	NP_742238.1. NC_002947.3.
3D structure databases
ProteinModelPortal	Q88RR1.
SMR	Q88RR1. Positions 2-168.
ModBase	Search...
Protein-protein interaction databases
STRING	Q88RR1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1043549.
GenomeReviews	Gene locus PP_0068 in contig AE015451_GR.
KEGG	ppu:PP_0068.
NMPDR	fig|160488.1.peg.68.
PATRIC	19938108. VBIPsePut30601_0073.
TIGR	PP_0068.
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HBG665227.
OMA	QKIVDDM.
PhylomeDB	Q88RR1.
ProtClustDB	PRK00150.
Enzyme and pathway databases
BioCyc	PPUT160488:PP_0068-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_PSEPK

Accession

Primary (citable) accession number: Q88RR1

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2003
Last sequence update:	June 1, 2003
Last modified:	January 25, 2012
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program