Q8DP79 (DEF_STRR6) 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:	spr1310

Organism

Streptococcus pneumoniae (strain ATCC BAA-255 / R6) [Reference proteome] [HAMAP]

Taxonomic identifier

171101 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	203 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 Reference 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 – 203

203

Peptide deformylase HAMAP-Rule MF_00163

PRO_0000082858

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 – 90

9

Beta strand

103 – 117

15

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

Beta strand

189 – 191

3

Beta strand

199 – 202

4

Sequences

	Sequence		Length	Mass (Da)
	Q8DP79 [UniParc]. Last modified March 1, 2003. Version 1. Checksum: E332956982A67161	FASTA	203	22,692
	10 20 30 40 50 60 MSAIERITKA AHLIDMNDII REGNPTLRTV 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

[1]

"Genome of the bacterium Streptococcus pneumoniae strain R6." Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S., DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C., Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J., Lee L.N. , Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M., McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B., Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y., Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R., Rosteck P.R. Jr., Skatrud P.L., Glass J.I. J. Bacteriol. 183:5709-5717(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-255 / R6.

+

Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE007317 Genomic DNA. Translation: AAL00114.1.

PIR

E98035.

RefSeq

NP_358903.1. NC_003098.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2AI7	X-ray	2.00	A	1-203	[»]
2AIA	X-ray	1.70	A	1-202	[»]
2AIE	X-ray	1.70	P	1-202	[»]
4EOX	X-ray	1.78	P	1-203	[»]

ProteinModelPortal

Q8DP79.

SMR

Q8DP79. Positions 2-203.

ModBase

Search...

Protein-protein interaction databases

STRING

171101.spr1310.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAL00114; AAL00114; spr1310.

GeneID

934523.

KEGG

spr:spr1310.

PATRIC

19702614. VBIStrPne107296_1422.

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

BindingDB

Q8DP79.

EvolutionaryTrace

Q8DP79.

Entry information

Entry name

DEF_STRR6

Accession

Primary (citable) accession number: Q8DP79

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	March 1, 2003
Last modified:	May 1, 2013
This is version 75 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program