Q87KD5 (DEF1_VIBPA) 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:	VP3042

Organism

Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) [Complete proteome] [HAMAP]

Taxonomic identifier

223926 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio › Vibrio harveyi group › Vibrio parahaemolyticus

Protein attributes

Sequence length	172 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-Rule MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule 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: InterPro 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-Rule 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 [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: RIMD 2210633.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000031 Genomic DNA. Translation: BAC61305.1.
RefSeq	NP_799421.1. NC_004603.1.
3D structure databases
ProteinModelPortal	Q87KD5.
SMR	Q87KD5. Positions 2-168.
ModBase	Search...
Protein-protein interaction databases
STRING	223926.VP3042.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAC61305; BAC61305; BAC61305.
GeneID	1190641.
KEGG	vpa:VP3042.
PATRIC	20144368. VBIVibPar50997_2927.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HOG000243509.
KO	K01462.
OMA	EMDQYQE.
ProtClustDB	PRK00150.
Family and domain databases
Gene3D	3.90.45.10. 1 hit.
HAMAP	MF_00163. Pep_deformylase.
InterPro	IPR000181. Fmet_deformylase. IPR023635. Peptide_deformylase. [Graphical view]
PANTHER	PTHR10458. PTHR10458. 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_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:	May 1, 2013
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program