Peptide deformylase - Escherichia coli (strain K12)

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P0A6K3 (DEF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 79. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference 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-Rule MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H₂O = formate + methionyl peptide. HAMAP-Rule MF_00163
Cofactor	Binds 1 Fe²⁺ ion per monomer. Ref.7
Subunit structure	Monomer.
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 Reference proteome
Gene Ontology (GO)
Biological_process	N-terminal protein amino acid modification Inferred from direct assay PubMed 9374870. Source: EcoCyc co-translational protein modification Inferred from physical interaction PubMed 18288106. Source: EcoCyc translation Inferred from electronic annotation. Source: HAMAP
Molecular_function	ferrous iron binding Inferred from direct assay Ref.7. Source: EcoCyc peptide deformylase activity Inferred from direct assay PubMed 9374870. Source: EcoCyc zinc ion binding Inferred from direct assay PubMed 11985624 Ref.6 PubMed 8244948. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
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

Removed HAMAP-Rule MF_00163

Chain

2 – 169

168

Peptide deformylase HAMAP-Rule MF_00163

PRO_0000082779

Sites

Active site

134

Metal binding

Iron

Metal binding

133

Iron

Metal binding

137

Iron

Secondary structure

169

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A6K3 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: C485EB6C1D2D91B8
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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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY.
+	Additional computationally mapped references.

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

NP_417745.1. NC_000913.2.
YP_492146.1. NC_007779.1.

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	2-169	[»]
1XEN	X-ray	1.85	A	2-169	[»]
1XEO	X-ray	1.30	A	2-169	[»]
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	[»]
4AL2	X-ray	2.60	A/B/C	2-169	[»]
4AL3	X-ray	1.98	A	2-169	[»]

ProteinModelPortal

P0A6K3.

SMR

P0A6K3. Positions 2-168.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47953N.

IntAct

P0A6K3. 9 interactions.

STRING

511145.b3287.

Proteomic databases

PaxDb

P0A6K3.

PRIDE

P0A6K3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76312; AAC76312; b3287.
BAE78005; BAE78005; BAE78005.

GeneID

12934422.
947780.

KEGG

ecj:Y75_p3890.
eco:b3287.

PATRIC

32122006. VBIEscCol129921_3380.

Organism-specific databases

EchoBASE

EB1410.

EcoGene

EG11440. def.

Phylogenomic databases

eggNOG

COG0242.

HOGENOM

HOG000243509.

K01462.

OMA

IQIGVPR.

ProtClustDB

PRK00150.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11440-MONOMER.
ECOL316407:JW3248-MONOMER.
MetaCyc:EG11440-MONOMER.

SABIO-RK

P0A6K3.

Gene expression databases

Genevestigator

P0A6K3.

Family and domain databases

Gene3D

3.90.45.10. 1 hit.

HAMAP

MF_00163. Pep_deformylase.

InterPro

IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]

PANTHER

PTHR10458. PTHR10458. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PIRSF

PIRSF004749. Pep_def. 1 hit.

PRINTS

PR01576. PDEFORMYLASE.

SUPFAM

SSF56420. Fmet_deformylase. 1 hit.

TIGRFAMs

TIGR00079. pept_deformyl. 1 hit.

ProtoNet

Search...

Other

BindingDB

P0A6K3.

ChEMBL

CHEMBL4976.

EvolutionaryTrace

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:	May 1, 2013
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents