Q1CCX6 (DEF_YERPN) 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:	YPN_3827
ORF Names:	YP516_4349

Organism

Yersinia pestis bv. Antiqua (strain Nepal516) [Complete proteome] [HAMAP]

Taxonomic identifier

377628 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Yersinia › Yersinia pestis

Protein attributes

Sequence length	170 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 – 170	170	Peptide deformylase HAMAP-Rule MF_00163		PRO_0000301128
Sites
	Active site	134	1	By similarity
	Metal binding	91	1	Iron By similarity
	Metal binding	133	1	Iron By similarity
	Metal binding	137	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q1CCX6 [UniParc]. Last modified July 11, 2006. Version 1. Checksum: EB01048E0E2423A7	FASTA	170	19,391
	10 20 30 40 50 60 MSVLQVLHYP DERLRKIAAP VKEVNGEIQR IVDDMFETMY AEEGIGLAAT QVDVHQQIIV 70 80 90 100 110 120 IDISENRDQR LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE 130 140 150 160 170 LETDGLLAIC IQHEMDHLIG KLFVDYLSPL KRQRIRQKLE KMAKLNARAN

References

[1]	"Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen." Chain P.S.G., Hu P., Malfatti S.A., Radnedge L., Larimer F., Vergez L.M., Worsham P., Chu M.C., Andersen G.L. J. Bacteriol. 188:4453-4463(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Nepal516.
[2]	"Yersinia pestis Nepal516A whole genome shotgun sequencing project." Plunkett G. III, Anderson B.D., Baumler D.J., Burland V., Cabot E.L., Glasner J.D., Mau B., Neeno-Eckwall E., Perna N.T., Munk A.C., Tapia R., Green L.D., Rogers Y.C., Detter J.C., Bruce D.C., Brettin T.S. Submitted (APR-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000305 Genomic DNA. Translation: ABG20154.1. ACNQ01000019 Genomic DNA. Translation: EEO74741.1.
RefSeq	YP_649754.1. NC_008149.1.
3D structure databases
ProteinModelPortal	Q1CCX6.
SMR	Q1CCX6. Positions 2-169.
ModBase	Search...
Protein-protein interaction databases
STRING	377628.YPN_3827.
Proteomic databases
PRIDE	Q1CCX6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABG20154; ABG20154; YPN_3827. EEO74741; EEO74741; YP516_4349.
GeneID	4123298.
KEGG	ypn:YPN_3827.
PATRIC	18607781. VBIYerPes46733_4518.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HOG000243509.
KO	K01462.
OMA	IQIGVPR.
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_YERPN

Accession

Primary (citable) accession number: Q1CCX6
Secondary accession number(s): D1Q2I8

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	July 11, 2006
Last modified:	May 1, 2013
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program