B2S3Z6 (DEF_TREPS) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptide deformylase
Short name=PDF
EC=3.5.1.88

Alternative name(s):
Polypeptide deformylase

Gene names

Name:	def
Ordered Locus Names:	TPASS_0757

Organism

Treponema pallidum subsp. pallidum (strain SS14) [Complete proteome] [HAMAP]

Taxonomic identifier

455434 [NCBI]

Taxonomic lineage

Bacteria › Spirochaetes › Spirochaetales › Spirochaetaceae › Treponema

Protein attributes

Sequence length	162 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 – 162	162	Peptide deformylase HAMAP MF_00163		PRO_1000097357
Sites
	Active site	129	1	By similarity
	Metal binding	86	1	Iron By similarity
	Metal binding	128	1	Iron By similarity
	Metal binding	132	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	B2S3Z6 [UniParc]. Last modified July 1, 2008. Version 1. Checksum: 15AEA6C940819CC1	FASTA	162	18,323
	10 20 30 40 50 60 MELKFLGEPC LTTVSEPVSE VDEQLRAFIS GMFRVMRGAG GVGLAAPQVG RTVRVFVVDV 70 80 90 100 110 120 EHHVRAFINP QITAASEEQS SYEEGCLSIP HIYERVLRPR RVSVQYLDEN GKRCAVDADG 130 140 150 160 ILARVIQHEY DHLDGILFLD RIDEKRRDDA LRRYAALRGT IR

References

[1]

"Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays." Matejkova P., Strouhal M., Smajs D., Norris S.J., Palzkill T., Petrosino J.F., Sodergren E., Norton J.E., Singh J., Richmond T.A., Molla M.N., Albert T.J., Weinstock G.M. BMC Microbiol. 8:76-76(2008) [PubMed: 18482458] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: SS14.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000805 Genomic DNA. Translation: ACD71175.1.
RefSeq	YP_001933754.1. NC_010741.1.
3D structure databases
ProteinModelPortal	B2S3Z6.
ModBase	Search...
Protein-protein interaction databases
STRING	B2S3Z6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	6333575.
GenomeReviews	Gene locus TPASS_0757 in contig CP000805_GR.
KEGG	tpp:TPASS_0757.
PATRIC	20529299. VBITrePal10923_0800.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG665227.
OMA	NAMEEGC.
ProtClustDB	CLSK218851.
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

DEF_TREPS

Accession

Primary (citable) accession number: B2S3Z6

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 24, 2009
Last sequence update:	July 1, 2008
Last modified:	January 25, 2012
This is version 26 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program