P68771 (DEF_STRP1) 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:	SPy_1958, M5005_Spy1669

Organism

Streptococcus pyogenes serotype M1 [Complete proteome] [HAMAP]

Taxonomic identifier

301447 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Streptococcaceae › Streptococcus › Streptococcus pyogenes

Protein attributes

Sequence length	204 AA.
Sequence status	Complete.
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. 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	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: 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 – 204

204

Peptide deformylase HAMAP-Rule MF_00163

PRO_0000082859

Sites

Active site

175

1

By similarity

Metal binding

131

1

Iron By similarity

Metal binding

174

1

Iron By similarity

Metal binding

178

1

Iron By similarity

Secondary structure

1

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204

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 – 90

9

Beta strand

101 – 118

18

Beta strand

120 – 125

6

Beta strand

144 – 153

10

Beta strand

159 – 164

6

Helix

166 – 178

13

Turn

179 – 181

3

Helix

184 – 187

4

Beta strand

200 – 203

4

Sequences

	Sequence		Length	Mass (Da)
	P68771 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: 89F8EDE94D94DC05	FASTA	204	22,862
	10 20 30 40 50 60 MSAQDKLIKP SHLITMDDII REGNPTLRAV AKEVSLPLCD EDILLGEKMM QFLKHSQDPV 70 80 90 100 110 120 MAEKLGLRAG VGLAAPQIDV SKRIIAVLVP NLPDKEGNPP KEAYSWQEVL YNPKIVSHSV 130 140 150 160 170 180 QDAALSDGEG CLSVDRVVEG YVVRHARVTV DYYDKEGQQH RIKLKGYNAI VVQHEIDHIN 190 200 GVLFYDRINA KNPFETKEEL LILD

References

[1]

"Complete genome sequence of an M1 strain of Streptococcus pyogenes." Ferretti J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P., Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L. , White J., Yuan X., Clifton S.W., Roe B.A., McLaughlin R.E. Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700294 / SF370 / Serotype M1.

[2]

"Evolutionary origin and emergence of a highly successful clone of serotype M1 group A Streptococcus involved multiple horizontal gene transfer events." Sumby P., Porcella S.F., Madrigal A.G., Barbian K.D., Virtaneva K., Ricklefs S.M., Sturdevant D.E., Graham M.R., Vuopio-Varkila J., Hoe N.P., Musser J.M. J. Infect. Dis. 192:771-782(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-947 / MGAS5005 / Serotype M1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE004092 Genomic DNA. Translation: AAK34651.1.
CP000017 Genomic DNA. Translation: AAZ52287.1.

RefSeq

NP_269930.1. NC_002737.1.
YP_283032.1. NC_007297.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2OS3	X-ray	2.26	A	2-204	[»]

ProteinModelPortal

P68771.

SMR

P68771. Positions 2-204.

ModBase

Search...

Protein-protein interaction databases

STRING

160490.SPy_1958.

Proteomic databases

PaxDb

P68771.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK34651; AAK34651; SPy_1958.
AAZ52287; AAZ52287; M5005_Spy1669.

GeneID

3571223.
901633.

KEGG

spy:SPy_1958.
spz:M5005_Spy_1669.

PATRIC

19717319. VBIStrPyo79812_1705.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0242.

HOGENOM

HOG000243507.

KO

K01462.

OMA

LTSGEGC.

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...

Other

EvolutionaryTrace

P68771.

Entry information

Entry name

DEF_STRP1

Accession

Primary (citable) accession number: P68771
Secondary accession number(s): P82590, Q48WI8, Q99XY7

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 21, 2004
Last sequence update:	December 21, 2004
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