Peptide deformylase 2 - Pseudomonas putida (strain KT2440)

Preferred order of sections

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

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas ›

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.
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 – 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)

Tools

Q88EA7 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: 044749D0EE6738C8
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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

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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.

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...
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	RFADGFH.
ProtClustDB	PRK12846.
Enzyme and pathway databases
BioCyc	PPUT160488:GIXO-4560-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

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 1, 2013
This is version 65 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents