Reviewed, UniProtKB/Swiss-Prot P0A6K3 (DEF_ECOLI)

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:	fms
Ordered Locus Names:	b3287, JW3248

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	169 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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 per monomer. Ref.7
Subunit structure	Monomer. HAMAP MF_00163
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	N-terminal protein amino acid modification Ref.6 Inferred from direct assay. Source: UniProtKB co-translational protein modification Inferred from physical interaction. Source: UniProtKB translation Inferred from electronic annotation. Source: HAMAP
Molecular function	ferrous iron binding Ref.7 Inferred from direct assay. Source: UniProtKB peptide deformylase activity Ref.6 Inferred from direct assay. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Ref.6 Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rplD	P60723	1	EBI-548913,EBI-545597
usg	P08390	1	EBI-548913,EBI-548921
yaeB	P28634	1	EBI-548913,EBI-1114692

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed HAMAP MF_00163

Chain

2 – 169

168

Peptide deformylase HAMAP MF_00163

PRO_0000082779

Sites

Active site

134

1

HAMAP MF_00163

Metal binding

91

1

Iron HAMAP MF_00163

Metal binding

133

1

Iron HAMAP MF_00163

Metal binding

137

1

Iron HAMAP MF_00163

Secondary structure

1

.

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169

Helix Strand Turn

Details...

Helix

12 – 15

4

Helix

26 – 41

16

Beta strand

45 – 48

4

Helix

49 – 52

4

Beta strand

56 – 61

6

Beta strand

71 – 82

12

Beta strand

105 – 112

8

Beta strand

118 – 124

7

Helix

125 – 137

13

Turn

138 – 140

3

Helix

143 – 146

4

Helix

149 – 166

18

Sequences

	Sequence		Length	Mass (Da)
	P0A6K3-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: C485EB6C1D2D91B8	FASTA	169	19,328
	10 20 30 40 50 60 MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV 70 80 90 100 110 120 IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE 130 140 150 160 LEADGLLAIC IQHEMDHLVG KLFMDYLSPL KQQRIRQKVE KLDRLKARA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation." Mazel D., Pochet S., Marliere P. EMBO J. 13:914-923(1994) [PubMed: 8112305] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: K12.
[2]	"Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli." Guillon J.-M., Mechulam Y., Schmitter J.-M., Blanquet S., Fayat G. J. Bacteriol. 174:4294-4301(1992) [PubMed: 1624424] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / K37.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control." Meinnel T., Guillon J.-M., Mechulam Y., Blanquet S. J. Bacteriol. 175:993-1000(1993) [PubMed: 8432722] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16. Strain: K12 / K37.
[6]	"Enzymatic properties of Escherichia coli peptide deformylase." Meinnel T., Blanquet S. J. Bacteriol. 177:1883-1887(1995) [PubMed: 7896716] [Abstract] Cited for: CHARACTERIZATION.
[7]	"Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site." Groche D., Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F. Biochem. Biophys. Res. Commun. 246:342-346(1998) [PubMed: 9610360] [Abstract] Cited for: COFACTOR.
[8]	"A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase." Meinnel T., Blanquet S., Dardel F. J. Mol. Biol. 262:375-386(1996) [PubMed: 8845003] [Abstract] Cited for: STRUCTURE BY NMR.
[9]	"Solution structure of nickel-peptide deformylase." Dardel F., Ragusa S., Lazennec C., Blanquet S., Meinnel T. J. Mol. Biol. 280:501-513(1998) [PubMed: 9665852] [Abstract] Cited for: STRUCTURE BY NMR.
[10]	"Crystal structure of the Escherichia coli peptide deformylase." Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D. Biochemistry 36:13904-13909(1997) [PubMed: 9374869] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
[11]	Erratum Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D. Biochemistry 37:13042-13042(1998)
[12]	"Structure of peptide deformylase and identification of the substrate binding site." Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F. J. Biol. Chem. 273:11413-11416(1998) [PubMed: 9565550] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[13]	"Iron center, substrate recognition and mechanism of peptide deformylase." Becker A., Schlichting I., Kabsch W., Groche D., Schultz S., Wagner A.F. Nat. Struct. Biol. 5:1053-1058(1998) [PubMed: 9846875] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[14]	"Structural basis for the design of antibiotics targeting peptide deformylase." Hao B., Gong W., Rajagopalan P.T.R., Zhou Y., Pei D., Chan M.K. Biochemistry 38:4712-4719(1999) [PubMed: 10200158] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X77800 Genomic DNA. Translation: CAA54826.1.
X63666 Genomic DNA. Translation: CAA45206.1.
X65946 Genomic DNA. No translation available.
X77091 Genomic DNA. Translation: CAA54367.1.
U18997 Genomic DNA. Translation: AAA58084.1.
U00096 Genomic DNA. Translation: AAC76312.1.
AP009048 Genomic DNA. Translation: BAE78005.1.

PIR

S23107.

RefSeq

AP_004504.1.
NP_417745.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BS4	X-ray	1.90	A/B/C	2-169	[»]
1BS5	X-ray	2.50	A/B/C	2-169	[»]
1BS6	X-ray	2.10	A/B/C	2-169	[»]
1BS7	X-ray	2.50	A/B/C	2-169	[»]
1BS8	X-ray	2.20	A/B/C	2-169	[»]
1BSJ	X-ray	3.00	A	2-169	[»]
1BSK	X-ray	3.00	A	2-169	[»]
1BSZ	X-ray	1.90	A/B/C	2-169	[»]
1DEF	NMR	-	A	2-148	[»]
1DFF	X-ray	2.88	A	2-165	[»]
1DTF	model	-	A	1-169	[»]
1G27	X-ray	2.10	A/B/C	2-168	[»]
1G2A	X-ray	1.75	A/B/C	2-168	[»]
1ICJ	X-ray	1.90	A/B/C	2-169	[»]
1LRU	X-ray	2.10	A/B/C	2-168	[»]
1XEM	X-ray	1.76	A	1-169	[»]
1XEN	X-ray	1.85	A	1-169	[»]
1XEO	X-ray	1.30	A	1-169	[»]
2AI8	X-ray	1.70	A/B/C	2-168	[»]
2DEF	NMR	-	A	3-148	[»]
2DTF	model	-	A	1-169	[»]
2KMN	NMR	-	A	2-148	[»]
2VHM	X-ray	3.74	5	148-162	[»]
2W3T	X-ray	1.69	A	2-169	[»]
2W3U	X-ray	1.96	A	2-169	[»]
3K6L	X-ray	2.15	A/B/C	1-169	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A6K3. 9 interactions.

STRING

P0A6K3.

Genome annotation databases

GeneID

947780.

GenomeReviews

Gene locus JW3248 in contig AP009048_GR.
Gene locus b3287 in contig U00096_GR.

KEGG

ecj:JW3248.
eco:b3287.

Organism-specific databases

EchoBASE

EB1410.

EcoGene

EG11440. def.

CMR

Search...

Phylogenomic databases

eggNOG

COG0242.

HOGENOM

HBG665227.

OMA

ELKANDW.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11440-MONOMER.
ECOL168927:B3287-MONOMER.
MetaCyc:EG11440-MONOMER.

Gene expression databases

Genevestigator

P0A6K3.

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...

Other Resources

BindingDB

P0A6K3.

Entry information

Entry name

DEF_ECOLI

Accession

Primary (citable) accession number: P0A6K3
Secondary accession number(s): P27251, Q2M6V1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	January 23, 2007
Last modified:	February 9, 2010
This is version 52 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)