Q88EA7 (DEF2_PSEPK) Reviewed, UniProtKB/Swiss-Prot

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:	PP_4559

Organism

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

Taxonomic identifier

160488 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas putida group › Pseudomonas putida

Protein attributes

Sequence length	178 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. HAMAP-Rule 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-HAMAP
Molecular_function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from electronic annotation. Source: UniProtKB-HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 178	178	Peptide deformylase 2 HAMAP-Rule MF_00163		PRO_0000082821
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)
	Q88EA7 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 044749D0EE6738C8	FASTA	178	19,852
	10 20 30 40 50 60 MIRDILKMGD ERLLRIAPPV PEHMLGSAEL QQLIDDMFET MRHVGGVGLA APQVGIDLQL 70 80 90 100 110 120 VIFGFERSER YPDAEAVPQT ILLNPVITPT SSEVEDGWEG CLSVPGLRGV VPRFKHICYQ 130 140 150 160 170 GIDPQGSPIN RFADGFHARV VQHECDHLIG RLYPSRIQDF AKFGYTEVLF PGLEVSED

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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: KT2440.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE015451 Genomic DNA. Translation: AAN70132.1.
RefSeq	NP_746668.1. NC_002947.3.
3D structure databases
ProteinModelPortal	Q88EA7.
SMR	Q88EA7. Positions 2-168.
ModBase	Search...
MobiDB	Search...
Protein-protein interaction databases
STRING	160488.PP_4559.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAN70132; AAN70132; PP_4559.
GeneID	1046247.
KEGG	ppu:PP_4559.
PATRIC	19947850. VBIPsePut30601_4862.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HOG000243508.
KO	K01462.
OMA	RVCQVGD.
OrthoDB	EOG664CMF.
Enzyme and pathway databases
BioCyc	PPUT160488:GIXO-4646-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. SSF56420. 1 hit.
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DEF2_PSEPK

Accession

Primary (citable) accession number: Q88EA7

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 27, 2003
Last sequence update:	June 1, 2003
Last modified:	May 14, 2014
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program