Reviewed, UniProtKB/Swiss-Prot Q7MCQ2 (DEF1_VIBVY)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 1
      Short name=PDF 1
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase 1

Gene names

Name:	def1
Ordered Locus Names:	VVA1334

Organism

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

Taxonomic identifier

196600 [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 1 HAMAP MF_00163		PRO_0000082879
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)
	Q7MCQ2-1 [UniParc]. Last modified December 15, 2003. Version 1. Checksum: 223FCB42ECE863B1	FASTA	168	18,760
	10 20 30 40 50 60 MAVLEILTAP DPRLRVQSKE VTDVAAVQTL IDDLLETLYE TDNGVGLAAP QVGREEAIVV 70 80 90 100 110 120 IDLSENRDEP LVLVNPKVVS GSNKEMGQEG CLSVPDYYAD VERYTSVVVE ALDRNGKELR 130 140 150 160 IETSEFLAIV MQHEIDHLSG NLFIDYLSPL KQQMAMKKVK KHNKLRAR

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	BA000038 Genomic DNA. Translation: BAC97360.1.
RefSeq	NP_937390.1.
3D structure databases
SMR	Q7MCQ2. Positions 2-168.
ModBase	Search...
Protein-protein interaction databases
STRING	Q7MCQ2.
Genome annotation databases
GeneID	2622196.
GenomeReviews	Gene locus VVA1334 in contig BA000038_GR.
KEGG	vvy:VVA1334.
NMPDR	fig|196600.1.peg.4661.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HBG665227.
OMA	EFLAIVM.
Enzyme and pathway databases
BioCyc	VVUL196600:VVA1334-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

DEF1_VIBVY

Accession

Primary (citable) accession number: Q7MCQ2

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)