Reviewed, UniProtKB/Swiss-Prot P43522 (DEF_THETH)

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

Organism

Thermus thermophilus

Taxonomic identifier

274 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	192 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
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 – 192

192

Peptide deformylase HAMAP MF_00163

PRO_0000082867

Sites

Active site

146

1

By similarity

Metal binding

102

1

Iron By similarity

Metal binding

145

1

Iron By similarity

Metal binding

149

1

Iron By similarity

Secondary structure

1

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192

Helix Strand Turn

Details...

Helix

11 – 14

4

Helix

26 – 39

14

Beta strand

43 – 46

4

Helix

47 – 50

4

Beta strand

54 – 60

7

Turn

75 – 77

3

Beta strand

81 – 93

13

Beta strand

96 – 100

5

Beta strand

110 – 115

6

Beta strand

117 – 124

8

Beta strand

130 – 136

7

Helix

137 – 150

14

Helix

155 – 158

4

Helix

161 – 170

10

Helix

172 – 181

10

Sequences

	Sequence		Length	Mass (Da)
	P43522-1 [UniParc]. Last modified November 1, 1995. Version 1. Checksum: 665945183A251361	FASTA	192	22,092
	10 20 30 40 50 60 MVYPIRLYGD PVLRRKARPV EDFSGIKRLA EDMLETMFEA KGVGLAAPQI GLSQRLFVAV 70 80 90 100 110 120 EYADEPEGEE ERPLRELVRR VYVVANPVIT YREGLVEGTE GCLSLPGLYS EEVPRAERIR 130 140 150 160 170 180 VEYQDEEGRG RVLELEGYMA RVFQHEIDHL DGILFFERLP KPKREAFLEA NRAELVRFQK 190 EARALLKELS QG

References

[1]	"Characterization of the Thermus thermophilus locus encoding peptide deformylase and methionyl-tRNA(fMet) formyltransferase." Meinnel T., Blanquet S. J. Bacteriol. 176:7387-7390(1994) [PubMed: 7961514] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: VK1.
[2]	"Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion." Meinnel T., Lazennec C., Villoing S., Blanquet S. J. Mol. Biol. 267:749-761(1997) [PubMed: 9126850] [Abstract] Cited for: CHARACTERIZATION.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X79087 Genomic DNA. Translation: CAA55695.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1V3Y	X-ray	1.81	A/B	1-192	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

3.5.1.88. 245.

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_THETH

Accession

Primary (citable) accession number: P43522

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1995
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)