Reviewed, UniProtKB/Swiss-Prot Q87KD5 (DEF1_VIBPA)

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:	VP3042

Organism

Vibrio parahaemolyticus [Complete proteome] [HAMAP]

Taxonomic identifier

670 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	172 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 – 172	172	Peptide deformylase 1 HAMAP MF_00163		PRO_0000082875
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)
	Q87KD5-1 [UniParc]. Last modified May 23, 2003. Version 1. Checksum: 7B551ED4015A9E3C	FASTA	172	19,405
	10 20 30 40 50 60 MSVLQVLTFP DDRLRTVAKP VDAVTPEIQK IVDDMIETMY DEEGIGLAAT QVDIHKRIVV 70 80 90 100 110 120 IDISETRDEP MVLINPEILE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRDGKEFT 130 140 150 160 170 FEADDLLAIC VQHELDHLQG KLFVDYLSPL KRKRIQDKLA KIKRFNEKQQ NA

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
EMBLGenBankDDBJ	BA000031 Genomic DNA. Translation: BAC61305.1.
RefSeq	NP_799421.1.
3D structure databases
HSSP	HSSP built from PDB template 1DEF based on UniProtKB P27251.
SMR	Q87KD5. Positions 2-165.
ModBase	Search...
Genome annotation databases
GeneID	1190641.
GenomeReviews	Gene locus VP3042 in contig BA000031_GR.
KEGG	vpa:VP3042.
NMPDR	fig|223926.1.peg.3042.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q87KD5.
OMA	CIQHECD.
Enzyme and pathway databases
BioCyc	VPAR223926:VP3042-MON.
BRENDA	3.5.1.88. 3063.
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

DEF1_VIBPA

Accession

Primary (citable) accession number: Q87KD5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	May 23, 2003
Last modified:	November 3, 2009
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)