Reviewed, UniProtKB/Swiss-Prot Q7MGK6 (DEF2_VIBVY)

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:	VV3225

Organism

Vibrio vulnificus (strain YJ016) [Complete proteome] [HAMAP]

Taxonomic identifier

196600 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	202 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 – 202	202	Peptide deformylase 2 HAMAP MF_00163		PRO_0000082880
Sites
	Active site	166	1	By similarity
	Metal binding	123	1	Iron By similarity
	Metal binding	165	1	Iron By similarity
	Metal binding	169	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q7MGK6-1 [UniParc]. Last modified December 15, 2003. Version 1. Checksum: 95DF963B38BF060A	FASTA	202	23,099
	10 20 30 40 50 60 MLLGCCHLGY KMSRIEPTRF VLFRHSSTFR VHMSVLQVLT FPDDRLRTVA KPVEKVTPEI 70 80 90 100 110 120 QKIVDDMIET MYDEEGIGLA ATQVDIHQRI VVIDISESRN EPMVLINPEI LEKRGEDGIE 130 140 150 160 170 180 EGCLSVPGAR ALVPRAAEVT VKALDRDGHE FTLEADDLLA ICIQHELDHL QGKLFVDYLS 190 200 PLKRKRIQDK LAKIKRFNEK QR

References

[1]

"Comparative genome analysis of Vibrio vulnificus, a marine pathogen." Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L., Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P., Lee C.-T., Hor L.-I., Tsai S.-F. Genome Res. 13:2577-2587(2003) [PubMed: 14656965] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000037 Genomic DNA. Translation: BAC95989.1.
RefSeq	NP_936018.1.
3D structure databases
SMR	Q7MGK6. Positions 34-200.
ModBase	Search...
Protein-protein interaction databases
STRING	Q7MGK6.
Genome annotation databases
GeneID	2626101.
GenomeReviews	Gene locus VV3225 in contig BA000037_GR.
KEGG	vvy:VV3225.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HBG665227.
OMA	RQLVDDM.
Enzyme and pathway databases
BioCyc	VVUL196600:VV3225-MONOMER.
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_VIBVY

Accession

Primary (citable) accession number: Q7MGK6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	December 15, 2003
Last modified:	February 9, 2010
This is version 39 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)