Reviewed, UniProtKB/Swiss-Prot Q93LE9 (DEF_LEPIN)

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:	pdf
Ordered Locus Names:	LA_2438

Organism

Leptospira interrogans [Complete proteome] [HAMAP]

Taxonomic identifier

173 [NCBI]

Taxonomic lineage

Bacteria › Spirochaetes › Spirochaetales › Leptospiraceae › Leptospira

Protein attributes

Sequence length	178 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 MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP MF_00163
Cofactor	Binds 1 Fe2+ ion By similarity. HAMAP MF_00163
Subunit structure	Homodimer. Ref.3
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 – 178

178

Peptide deformylase HAMAP MF_00163

PRO_0000082795

Sites

Active site

145

1

By similarity

Metal binding

102

1

Iron By similarity

Metal binding

144

1

Iron By similarity

Metal binding

148

1

Iron By similarity

Secondary structure

1

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178

Helix Strand Turn

Details...

Helix

12 – 15

4

Helix

25 – 27

3

Helix

29 – 44

16

Beta strand

48 – 51

4

Helix

52 – 55

4

Beta strand

59 – 64

6

Beta strand

70 – 72

3

Beta strand

81 – 90

10

Beta strand

98 – 100

3

Beta strand

108 – 112

5

Beta strand

115 – 123

9

Beta strand

129 – 135

7

Helix

136 – 149

14

Helix

154 – 157

4

Beta strand

163 – 166

4

Helix

167 – 171

5

Sequences

	Sequence		Length	Mass (Da)
	Q93LE9-1 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 8F6F3D2449A48B10	FASTA	178	20,379
	10 20 30 40 50 60 MSVRKILRMG DPILRKISEP VTEDEIQTKE FKKLIRDMFD TMRHAEGVGL AAPQIGILKQ 70 80 90 100 110 120 IVVVGSEDNE RYPGTPDVPE RIILNPVITP LTKDTSGFWE GCLSVPGMRG YVERPNQIRM 130 140 150 160 170 QWMDEKGNQF DETIDGYKAI VYQHECDHLQ GILYVDRLKD TKLFGFNETL DSSHNVLD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, high-level expression, purification and crystallization of peptide deformylase from Leptospira interrogans." Li Y., Ren S., Gong W. Acta Crystallogr. D 58:846-848(2002) [PubMed: 11976499] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CRYSTALLIZATION. Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.
[2]	"Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing." Ren S.-X., Fu G., Jiang X.-G., Zeng R., Miao Y.-G., Xu H., Zhang Y.-X., Xiong H., Lu G., Lu L.-F., Jiang H.-Q., Jia J., Tu Y.-F., Jiang J.-X., Gu W.-Y., Zhang Y.-Q., Cai Z., Sheng H.-H. , Yin H.-F., Zhang Y., Zhu G.-F., Wan M., Huang H.-L., Qian Z., Wang S.-Y., Ma W., Yao Z.-J., Shen Y., Qiang B.-Q., Xia Q.-C., Guo X.-K., Danchin A., Saint Girons I., Somerville R.L., Wen Y.-M., Shi M.-H., Chen Z., Xu J.-G., Zhao G.-P. Nature 422:888-893(2003) [PubMed: 12712204] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 56601 / Serogroup Icterohaemorrhagiae / Serovar lai.
[3]	"Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans." Zhou Z., Song X., Li Y., Gong W. J. Mol. Biol. 339:207-215(2004) [PubMed: 15123432] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT. Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY040678 Genomic DNA. Translation: AAK70806.1.
AE010300 Genomic DNA. Translation: AAN49637.1.

RefSeq

NP_712619.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SV2	X-ray	3.00	A/B	2-178	[»]
1SZZ	X-ray	3.30	A/B/C/D/E/F/G/H	2-178	[»]
1VEV	X-ray	2.51	A/B	2-178	[»]
1VEY	X-ray	3.30	A/B	2-178	[»]
1VEZ	X-ray	2.30	A/B	2-178	[»]
1Y6H	X-ray	2.20	A/B	2-178	[»]

ModBase

Search...

Genome annotation databases

GeneID

1151781.

GenomeReviews

Gene locus LA_2438 in contig AE010300_GR.

KEGG

lil:LA2438.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG665227.

OMA

HNERYPD.

Enzyme and pathway databases

BioCyc

LINT-130-01:LINT-130-01-001471-MONOMER.
LINT189518:LA2438-MONOMER.

BRENDA

3.5.1.88. 258108.

Family and domain databases

HAMAP

MF_00163. Pep_deformylase.
[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.

TIGRFAMs

TIGR00079. pept_deformyl. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DEF_LEPIN

Accession

Primary (citable) accession number: Q93LE9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2002
Last sequence update:	December 1, 2001
Last modified:	February 9, 2010
This is version 59 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)