Reviewed, UniProtKB/Swiss-Prot Q819U0 (DEF1_BACCR)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 1
      Short name=PDF 1
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase 1

Gene names

Name:	def1
Ordered Locus Names:	BC_3865

Organism

Bacillus cereus (strain ATCC 14579 / DSM 31) [Complete proteome] [HAMAP]

Taxonomic identifier

226900 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus › Bacillus cereus group

Protein attributes

Sequence length	156 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 Complete proteome
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 – 156

156

Peptide deformylase 1 HAMAP MF_00163

PRO_0000082735

Sites

Active site

133

1

By similarity

Metal binding

90

1

Iron By similarity

Metal binding

132

1

Iron By similarity

Metal binding

136

1

Iron By similarity

Secondary structure

1

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156

Helix Strand Turn

Details...

Helix

12 – 15

4

Helix

26 – 41

16

Beta strand

45 – 48

4

Helix

49 – 52

4

Beta strand

56 – 62

7

Turn

65 – 67

3

Beta strand

69 – 88

20

Beta strand

98 – 111

14

Beta strand

117 – 123

7

Helix

124 – 137

14

Helix

142 – 144

3

Beta strand

146 – 149

4

Sequences

	Sequence		Length	Mass (Da)
	Q819U0-1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 0B68AB39485C4D8A	FASTA	156	17,480
	10 20 30 40 50 60 MAVLEIIKHP NEVLETPCER VINFDKKLVK LLKDMHETML IADGVGLAAP QVGVSLQVAV 70 80 90 100 110 120 VDVDDDTGKI ELINPSILEK RGEQVGPEGC LSFPGLYGEV ERADYIKVRA QNRRGKVFLL 130 140 150 EAEGFLARAI QHEIDHLHGV LFTSKVTRYY EENELE

References

[1]

"Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis." Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V., Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M., Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch G. , Haselkorn R., Fonstein M., Ehrlich S.D., Overbeek R., Kyrpides N.C. Nature 423:87-91(2003) [PubMed: 12721630] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

+

Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AE016877 Genomic DNA. Translation: AAP10787.1.

RefSeq

NP_833586.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WS0	X-ray	1.70	A	1-156	[»]
1WS1	X-ray	2.00	A	1-156	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q819U0.

Genome annotation databases

GeneID

1206210.

GenomeReviews

Gene locus BC_3865 in contig AE016877_GR.

KEGG

bce:BC3865.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q819U0.

OMA

IGVPRRM.

Enzyme and pathway databases

BioCyc

BCER226900:BC_3865-MON.

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

DEF1_BACCR

Accession

Primary (citable) accession number: Q819U0

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	June 1, 2003
Last modified:	November 3, 2009
This is version 44 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)