P56419 (DEF_HELPY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Alternative name(s):
Polypeptide deformylase

Gene names

Name:	def
Ordered Locus Names:	HP_0793

Organism

Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]

Taxonomic identifier

85962 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Helicobacter › Helicobacter pylori

Protein attributes

Sequence length	174 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 Reference 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 – 174	174	Peptide deformylase HAMAP-Rule MF_00163		PRO_0000082790
Sites
	Active site	139	1	By similarity
	Metal binding	96	1	Iron By similarity
	Metal binding	138	1	Iron By similarity
	Metal binding	142	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	P56419 [UniParc]. Last modified July 15, 1998. Version 1. Checksum: 375525F45E5CC774	FASTA	174	20,057
	10 20 30 40 50 60 MALLEIIHYP SKILRTISKE VVSFDSKLHQ QLDDMHETMI ASEGIGLAAI QVGLPLRMLI 70 80 90 100 110 120 INLPQEDGVQ HKEDCLEIIN PKFIETGGSM MYREGCLSVP GFYEEVERFE KVKIEYQNRF 130 140 150 160 170 AEVKVLEASE LLAVAIQHEI DHLNGVLFVD KLSILKRKKF EKELKELQKK QKHE

References

[1]

"The complete genome sequence of the gastric pathogen Helicobacter pylori." Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C. Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700392 / 26695.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE000511 Genomic DNA. Translation: AAD07841.1.
PIR	A64619.
RefSeq	NP_207586.1. NC_000915.1. YP_006934707.1. NC_018939.1.
3D structure databases
ProteinModelPortal	P56419.
SMR	P56419. Positions 2-167.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-3266N.
MINT	MINT-165640.
STRING	85962.HP0793.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAD07841; AAD07841; HP_0793.
GeneID	13869976. 899348.
KEGG	heo:C694_04065. hpy:HP0793.
PATRIC	20592873. VBIHelPyl33062_0825.
Phylogenomic databases
eggNOG	COG0242.
KO	K01462.
OMA	LEIIHYP.
ProtClustDB	PRK00150.
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

DEF_HELPY

Accession

Primary (citable) accession number: P56419

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	July 15, 1998
Last modified:	May 1, 2013
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program