Q8DDE3 (DEF1_VIBVU) Reviewed, UniProtKB/Swiss-Prot

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:	VV1_1048

Organism

Vibrio vulnificus [Complete proteome] [HAMAP]

Taxonomic identifier

672 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

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 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: UniProtKB-KW
Molecular function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 170	170	Peptide deformylase 1 HAMAP MF_00163		PRO_0000082877
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)
	Q8DDE3 [UniParc]. Last modified March 1, 2003. Version 1. Checksum: A03A4C710F0B3BC2	FASTA	170	19,293
	10 20 30 40 50 60 MSVLQVLTFP DDRLRTVAKP VEKVTPEIQK IVDDMIETMY DEEGIGLAAT QVDIHQRIVV 70 80 90 100 110 120 IDISESRNEP MVLINPEILE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRDGHEFT 130 140 150 160 170 LEADDLLAIC IQHELDHLQG KLFVDYLSPL KRKRIQDKLA KIKRFNEKQR

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
EMBL GenBank DDBJ	AE016795 Genomic DNA. Translation: AAO09535.1.
RefSeq	NP_760008.1. NC_004459.3.
3D structure databases
ProteinModelPortal	Q8DDE3.
SMR	Q8DDE3. Positions 2-168.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1177981.
GenomeReviews	Gene locus VV1_1048 in contig AE016795_GR.
KEGG	vvu:VV1_1048.
PATRIC	20158909. VBIVibVul94426_1005.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG665227.
OMA	QKIVDDM.
ProtClustDB	PRK00150.
Enzyme and pathway databases
BioCyc	VVUL216895:VV1_1048-MONOMER.
Family and domain databases
HAMAP	MF_00163. Pep_deformylase. [Tree]
InterPro	IPR000181. Fmet_deformylase. IPR023635. Peptide_deformylase. [Graphical view]
Gene3D	G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
KO	K01462.
PANTHER	PTHR10458. Fmet_deformylase. 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

DEF1_VIBVU

Accession

Primary (citable) accession number: Q8DDE3

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	March 1, 2003
Last modified:	January 25, 2012
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