Reviewed, UniProtKB/Swiss-Prot Q8D5P5 (DEF2_VIBVU)

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:	VV2_0863

Organism

Vibrio vulnificus [Complete proteome] [HAMAP]

Taxonomic identifier

672 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	168 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP 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: 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_0000082878
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)
	Q8D5P5-1 [UniParc]. Last modified March 1, 2003. Version 1. Checksum: D835D1F2ECFF68DC	FASTA	168	18,729
	10 20 30 40 50 60 MAVLEILTAP DPRLRVQSKE VTDVAAVQTL IDDLLETLYE TDNGVGLAAP QVGREEAIVV 70 80 90 100 110 120 IDLSENRDEP LVLVNPKVVS GSNKEMGQEG CLSVPDYYAD VERYTSVVVE ALDRDGKPLR 130 140 150 160 IETSEFLAIV MQHEIDHLSG NLFIDYLSPL KQQMAMKKVK KHNKLRAR

References

[1]	"Complete genome sequence of Vibrio vulnificus CMCP6." Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E. Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CMCP6.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE016796 Genomic DNA. Translation: AAO07786.1.
RefSeq	NP_762796.1.
3D structure databases
HSSP	HSSP built from PDB template 1LRU based on UniProtKB P27251.
ModBase	Search...
Genome annotation databases
GeneID	1180842.
GenomeReviews	Gene locus VV2_0863 in contig AE016796_GR.
KEGG	vvu:VV2_0863.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q8D5P5.
OMA	Q8D5P5. SENRDEP.
Enzyme and pathway databases
BioCyc	VVUL216895:VV2_0863-MON.
BRENDA	3.5.1.88. 277169.
Family and domain databases
HAMAP	MF_00163. [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.
ProDom	PD003844. Fmet_deformylase. 1 hit. [Graphical view] [Entries sharing at least one domain]
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DEF2_VIBVU

Accession

Primary (citable) accession number: Q8D5P5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	March 1, 2003
Last modified:	June 16, 2009
This is version 37 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)