P68826 (DEF_STAAU) 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
Synonyms:	def1, pdf1

Organism

Staphylococcus aureus

Taxonomic identifier

1280 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Staphylococcaceae › Staphylococcus

Protein attributes

Sequence length	183 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.
Mass spectrometry	Molecular mass is 20600 Da from positions 1 - 183. Determined by MALDI. Ref.2

Ontologies

Keywords
Biological process	Protein biosynthesis
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure
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 – 183

183

Peptide deformylase HAMAP-Rule MF_00163

PRO_0000082843

Sites

Active site

155

1

By similarity

Metal binding

111

1

Iron

Metal binding

154

1

Iron

Metal binding

158

1

Iron

Secondary structure

1

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183

Helix Strand Turn

Details...

Helix

4 – 6

3

Helix

13 – 16

4

Helix

28 – 45

18

Helix

47 – 53

7

Beta strand

58 – 62

5

Helix

63 – 66

4

Beta strand

70 – 77

8

Beta strand

81 – 83

3

Beta strand

86 – 98

13

Beta strand

100 – 104

5

Beta strand

124 – 133

10

Beta strand

139 – 145

7

Helix

146 – 159

14

Helix

164 – 167

4

Beta strand

170 – 172

3

Sequences

	Sequence		Length	Mass (Da)
	P68826 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: 32A64066A6FEAB0E	FASTA	183	20,559
	10 20 30 40 50 60 MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA KRYGLRSGVG 70 80 90 100 110 120 LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV QEAYLPTGEG CLSVDDNVAG 130 140 150 160 170 180 LVHRHNRITI KAKDIEGNDI QLRLKGYPAI VFQHEIDHLN GVMFYDHIDK NHPLQPHTDA VEV

References

[1]	"Staphylococcus aureus deformylase 1 encoding DNA." Lonetto M.A., Sylvester D.R., Warren R.L. Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: WCUH29 / NCIMB 40771.
[2]	"Identification of Staphylococcus aureus proteins recognized by the antibody-mediated immune response to a biofilm infection." Brady R.A., Leid J.G., Camper A.K., Costerton J.W., Shirtliff M.E. Infect. Immun. 74:3415-3426(2006) [PubMed] [Europe PMC] [Abstract] Cited for: MASS SPECTROMETRY. Strain: MRSA-M2.
[3]	"Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase." Kreusch A., Spraggon G., Lee C.C., Klock H., McMullan D., Ng K., Shin T., Vincent J., Warner I., Ericson C., Lesley S.A. J. Mol. Biol. 330:309-321(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY007227 Genomic DNA. Translation: AAG02249.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1LM4	X-ray	1.45	A/B	1-183	[»]
1LMH	X-ray	1.90	A	1-183	[»]
1LQW	X-ray	1.87	A/B	1-183	[»]
1Q1Y	X-ray	1.90	A	1-183	[»]
2AI9	X-ray	2.50	A/B	1-183	[»]

ProteinModelPortal

P68826.

SMR

P68826. Positions 1-183.

ModBase

Search...

Proteomic databases

PRIDE

P68826.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Phylogenomic databases

eggNOG

COG0242.

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

P68826.

EvolutionaryTrace

P68826.

Entry information

Entry name

DEF_STAAU

Accession

Primary (citable) accession number: P68826
Secondary accession number(s): Q9F4L4

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 21, 2004
Last sequence update:	December 21, 2004
Last modified:	April 3, 2013
This is version 47 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program