Reviewed, UniProtKB/Swiss-Prot Q87I22 (DEF2_VIBPA)

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:	VPA0784

Organism

Vibrio parahaemolyticus [Complete proteome] [HAMAP]

Taxonomic identifier

670 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

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: HAMAP
Molecular function	iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW 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 – 168	168	Peptide deformylase 2 HAMAP MF_00163		PRO_0000082876
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)
	Q87I22-1 [UniParc]. Last modified May 23, 2003. Version 1. Checksum: D71655F48CE28EE6	FASTA	168	18,491
	10 20 30 40 50 60 MAVLEILSIP DPRLKVKAEK VTDVSTIQTL IDDMLETLYA TGNGIGLAST QVGRKEAVVV 70 80 90 100 110 120 IDISDERNDP LILVNPEVVS GENKALGQEG CLSVPEYYAD VERYTSVVVS ALDRDGNPIT 130 140 150 160 IESDEFLAIV MQHEIDHLSG NLFIDYLSPL KQKMAMKKVK KYVKAQAK

References

[1]

"Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae." Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T. Lancet 361:743-749(2003) [PubMed: 12620739] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: RIMD 2210633 / Serotype O3:K6.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000032 Genomic DNA. Translation: BAC62127.1.
RefSeq	NP_800294.1.
3D structure databases
SMR	Q87I22. Positions 2-168.
ModBase	Search...
Genome annotation databases
GeneID	1191473.
GenomeReviews	Gene locus VPA0784 in contig BA000032_GR.
KEGG	vpa:VPA0784.
NMPDR	fig|223926.1.peg.3864.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG665227.
OMA	EFLAIVM.
Enzyme and pathway databases
BioCyc	VPAR223926:VPA0784-MONOMER.
BRENDA	3.5.1.88. 3063.
Family and domain databases
HAMAP	MF_00163. Pep_deformylase. [Tree]
InterPro	IPR000181. Fmet_deformylase. [Graphical view]
Gene3D	G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
PANTHER	PTHR10458. Fmet_deformylase. 1 hit.
Pfam	PF01327. Pep_deformylase. 1 hit. [Graphical view]
PIRSF	PIRSF004749. Pep_def. 1 hit.
PRINTS	PR01576. PDEFORMYLASE.
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DEF2_VIBPA

Accession

Primary (citable) accession number: Q87I22

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	May 23, 2003
Last modified:	February 9, 2010
This is version 42 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)