Reviewed, UniProtKB/Swiss-Prot Q9F2F0 (DEF_STRPN)

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:	SP_1456

Organism

Streptococcus pneumoniae [Complete proteome] [HAMAP]

Taxonomic identifier

1313 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Streptococcus

Protein attributes

Sequence length	203 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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	3D-structure 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 – 203

203

Peptide deformylase HAMAP MF_00163

PRO_0000082857

Sites

Active site

174

1

By similarity

Metal binding

130

1

Iron By similarity

Metal binding

173

1

Iron By similarity

Metal binding

177

1

Iron By similarity

Secondary structure

1

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203

Helix Strand Turn

Details...

Helix

3 – 7

5

Helix

16 – 18

3

Helix

25 – 28

4

Helix

40 – 56

17

Helix

59 – 65

7

Beta strand

71 – 74

4

Helix

75 – 78

4

Beta strand

82 – 89

8

Beta strand

105 – 117

13

Beta strand

119 – 124

6

Beta strand

143 – 145

3

Beta strand

147 – 152

6

Beta strand

158 – 163

6

Helix

165 – 178

14

Helix

183 – 186

4

Sequences

	Sequence		Length	Mass (Da)
	Q9F2F0-1 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: 192F91B42375F8CD	FASTA	203	22,676
	10 20 30 40 50 60 MSAIERITKA AHLIDMNDII REGNPTLRAI AEEVTFPLSD QEIILGEKMM QFLKHSQDPV 70 80 90 100 110 120 MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ EAYDLEAIMY NPKIVSHSVQ 130 140 150 160 170 180 DAALGEGEGC LSVDRNVPGY VVRHARVTVD YFDKDGEKHR IKLKGYNSIV VQHEIDHING 190 200 IMFYDRINEK DPFAVKDGLL ILE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Peptide deformylase as an antibacterial drug target: target validation and resistance development." Apfel C.M., Locher H., Evers S., Takacs B., Hubschwerlen C., Pirson W., Page M.G., Keck W. Antimicrob. Agents Chemother. 45:1058-1064(2001) [PubMed: 11257016] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete genome sequence of a virulent isolate of Streptococcus pneumoniae." Tettelin H., Nelson K.E., Paulsen I.T., Eisen J.A., Read T.D., Peterson S.N., Heidelberg J.F., DeBoy R.T., Haft D.H., Dodson R.J., Durkin A.S., Gwinn M.L., Kolonay J.F., Nelson W.C., Peterson J.D., Umayam L.A., White O., Salzberg S.L. , Lewis M.R., Radune D., Holtzapple E.K., Khouri H.M., Wolf A.M., Utterback T.R., Hansen C.L., McDonald L.A., Feldblyum T.V., Angiuoli S.V., Dickinson T., Hickey E.K., Holt I.E., Loftus B.J., Yang F., Smith H.O., Venter J.C., Dougherty B.A., Morrison D.A., Hollingshead S.K., Fraser C.M. Science 293:498-506(2001) [PubMed: 11463916] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-334 / TIGR4.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AJ278785 Genomic DNA. Translation: CAC15392.1.
AE005672 Genomic DNA. Translation: AAK75550.1.

PIR

E95169.

RefSeq

NP_345910.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1LM6	X-ray	1.75	A	1-203	[»]

ModBase

Search...

Genome annotation databases

GeneID

931384.

GenomeReviews

Gene locus SP_1456 in contig AE005672_GR.

KEGG

spn:SP_1456.

TIGR

SP_1456.

Phylogenomic databases

HOGENOM

Q9F2F0.

OMA

Q9F2F0. EGMLILE.

Enzyme and pathway databases

BRENDA

3.5.1.88. 600.

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

DEF_STRPN

Accession

Primary (citable) accession number: Q9F2F0

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 5, 2001
Last sequence update:	March 1, 2001
Last modified:	June 16, 2009
This is version 58 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)