Reviewed, UniProtKB/Swiss-Prot O31410 (DEF2_BACST)

Names and origin

Protein names	Recommended name:     Peptide deformylase 2       Short name=PDF 2     EC=3.5.1.88 Alternative name(s):     Polypeptide deformylase 2
Organism	Bacillus stearothermophilus (Geobacillus stearothermophilus)
Taxonomic identifier	1422 [NCBI]
Taxonomic lineage	Bacteria › Firmicutes › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	184 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. HAMAP MF_00163
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 – 184

184

Peptide deformylase 2 HAMAP MF_00163

PRO_0000082738

Sites

Active site

154

1

By similarity

Metal binding

110

1

Iron By similarity

Metal binding

153

1

Iron By similarity

Metal binding

157

1

Iron By similarity

Secondary structure

1

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184

Helix Strand Turn

Details...

Helix

4 – 6

3

Helix

13 – 16

4

Helix

28 – 44

17

Helix

47 – 53

7

Beta strand

59 – 62

4

Helix

63 – 66

4

Beta strand

70 – 78

9

Beta strand

84 – 97

14

Beta strand

99 – 104

6

Beta strand

123 – 132

10

Beta strand

138 – 144

7

Helix

145 – 158

14

Helix

163 – 166

4

Beta strand

180 – 182

3

Sequences

	Sequence		Length	Mass (Da)
	O31410-1 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: 9CD85DEE53632FA0	FASTA	184	20,383
	10 20 30 40 50 60 MITMKDIIKE GHPTLRKVAE PVPLPPSEED KRILQSLLDY VKMSQDPELA AKYGLRPGIG 70 80 90 100 110 120 LAAPQINVSK RMIAVHVTDE NGTLYSYALF NPKIVSHSVQ QCYLTTGEGC LSVDRDVPGY 130 140 150 160 170 180 VLRYARITVT GTTLDGEEVT LRLKGLPAIV FQHEIDHLNG IMFYDRINPA DPFQVPDGAI PIGR

References

[1]	"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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: ATCC 1518.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

Y10549 Genomic DNA. Translation: CAA71581.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1LQY	X-ray	1.90	A	1-184	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

3.5.1.88. 266715.

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

DEF2_BACST

Accession

Primary (citable) accession number: O31410

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 1, 1998
Last modified:	June 16, 2009
This is version 61 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)