Q9FV53 (DEF1A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptide deformylase 1A, chloroplastic/mitochondrial
Short name=AtDEF1
Short name=AtPDF1A
Short name=PDF 1A
EC=3.5.1.88

Alternative name(s):
Polypeptide deformylase

Gene names

Name:	PDF1A
Synonyms:	DEF1
Ordered Locus Names:	At1g15390
ORF Names:	F9L1.34, F9L1_34

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	269 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. Ref.1
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
Cofactor	Binds 1 Zinc ion per subunit. Ref.6
Enzyme regulation	Inhibited by actinonin. Ref.5 Ref.6
Subunit structure	Homodimer. Ref.8
Subcellular location	Plastid › chloroplast stroma. Mitochondrion. Note: Reported to be localized to mitochondria, based on transient GFP expression in a heterologous system (Ref.1), but also shown to be imported and correctly processed in isolated chloroplast (Ref.5). Ref.1 Ref.5
Tissue specificity	Expressed in roots, leaves, flowers and siliques. Ref.1
Disruption phenotype	No visible phenotype. Ref.7
Sequence similarities	Belongs to the polypeptide deformylase family.
Biophysicochemical properties	Kinetic parameters: KM=240 µM for N-formyl-Met-Leu-rho-nitroanilide Ref.5 KM=710 µM for N-formyl-Met-Ala-Ser Vmax=0.11 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide Vmax=0.20 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser
Sequence caution	The sequence AAD39667.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence AAK32873.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Chloroplast Mitochondrion Plastid
Domain	Transit peptide
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	co-translational protein modification Inferred from direct assay Ref.6. Source: TAIR translation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	chloroplast Inferred from direct assay PubMed 18431481. Source: TAIR chloroplast stroma Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Inferred from direct assay Ref.1PubMed 18385124. Source: TAIR plant-type cell wall Inferred from direct assay PubMed 16287169. Source: TAIR
Molecular_function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from direct assay Ref.6. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 60

60

Chloroplast and mitochondrion Potential

Chain

61 – 269

209

Peptide deformylase 1A, chloroplastic/mitochondrial

PRO_0000006730

Regions

Region

123 – 126

4

Substrate binding

Region

191 – 196

6

Dimerization

Region

236 – 254

19

Dimerization

Sites

Active site

231

1

Metal binding

188

1

Zinc

Metal binding

230

1

Zinc

Metal binding

234

1

Zinc

Binding site

187

1

Substrate; via carbonyl oxygen

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

269

Helix Strand Turn

Details...

Helix

89 – 91

3

Turn

100 – 104

5

Helix

106 – 121

16

Beta strand

125 – 128

4

Helix

129 – 132

4

Beta strand

136 – 143

8

Helix

145 – 149

5

Helix

153 – 158

6

Beta strand

164 – 179

16

Beta strand

181 – 188

8

Beta strand

191 – 209

19

Beta strand

215 – 221

7

Helix

222 – 235

14

Helix

240 – 242

3

Helix

252 – 254

3

Sequences

	Sequence		Length	Mass (Da)
	Q9FV53 [UniParc]. Last modified May 31, 2011. Version 3. Checksum: BDDF13CC38F319C3	FASTA	269	29,996
	10 20 30 40 50 60 MGLHRDEATA METLFRVSLR LLPVSAAVTC RSIRFPVSRP GSSHLLNRKL YNLPTSSSSS 70 80 90 100 110 120 LSTKAGWLLG LGEKKKKVDL PEIVASGDPV LHEKAREVDP GEIGSERIQK IIDDMIKVMR 130 140 150 160 170 180 LAPGVGLAAP QIGVPLRIIV LEDTKEYISY APKEEILAQE RRHFDLMVMV NPVLKERSNK 190 200 210 220 230 240 KALFFEGCLS VDGFRAAVER YLEVVVTGYD RQGKRIEVNA SGWQARILQH ECDHLDGNLY 250 260 VDKMVPRTFR TVDNLDLPLA EGCPKLGPQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms." Giglione C., Serero A., Pierre M., Boisson B., Meinnel T. EMBO J. 19:5916-5929(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 6-269. Strain: cv. Columbia.
[5]	"Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis." Dirk L.M., Williams M.A., Houtz R.L. Plant Physiol. 127:97-107(2001) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[6]	"Distinctive features of the two classes of eukaryotic peptide deformylases." Serero A., Giglione C., Meinnel T. J. Mol. Biol. 314:695-708(2001) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR, ENZYME REGULATION.
[7]	"Control of protein life-span by N-terminal methionine excision." Giglione C., Vallon O., Meinnel T. EMBO J. 22:13-23(2003) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[8]	"The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms." Fieulaine S., Juillan-Binard C., Serero A., Dardel F., Giglione C., Meinnel T., Ferrer J.-L. J. Biol. Chem. 280:42315-42324(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 79-267 IN COMPLEX WITH ZINC IONS AND SUBSTRATE, HOMODIMERIZATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF250959 mRNA. Translation: AAG33973.1.
AC007591 Genomic DNA. Translation: AAD39667.1. Different initiation.
CP002684 Genomic DNA. Translation: AEE29315.1.
AF361861 mRNA. Translation: AAK32873.1. Different initiation.
AY129485 mRNA. Translation: AAM91071.1.

IPI

IPI00534874.

PIR

E86288.

RefSeq

NP_563974.1. NM_101408.2.

UniGene

At.11423.
At.19791.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZXZ	X-ray	2.80	A/B	79-267	[»]
1ZY0	X-ray	2.90	A/B	79-267	[»]
1ZY1	X-ray	3.00	A/B	79-267	[»]

ProteinModelPortal

Q9FV53.

SMR

Q9FV53. Positions 79-267.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT1G15390.1-P.

Proteomic databases

PaxDb

Q9FV53.

PRIDE

Q9FV53.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT1G15390.1; AT1G15390.1; AT1G15390.

GeneID

838109.

KEGG

ath:AT1G15390.

Organism-specific databases

TAIR

At1g15390.

Phylogenomic databases

eggNOG

COG0242.

HOGENOM

HOG000243508.

InParanoid

Q9FV53.

KO

K01462.

OMA

LTSGEGC.

ProtClustDB

CLSN2687814.

Enzyme and pathway databases

SABIO-RK

Q9FV53.

Gene expression databases

Genevestigator

Q9FV53.

GermOnline

AT1G15390. Arabidopsis thaliana.

Family and domain databases

Gene3D

3.90.45.10. 1 hit.

InterPro

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

PANTHER

PTHR10458. PTHR10458. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PRINTS

PR01576. PDEFORMYLASE.

SUPFAM

SSF56420. Fmet_deformylase. 1 hit.

TIGRFAMs

TIGR00079. pept_deformyl. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1075041.

EvolutionaryTrace

Q9FV53.

Entry information

Entry name

DEF1A_ARATH

Accession

Primary (citable) accession number: Q9FV53
Secondary accession number(s): Q9XI30

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 5, 2001
Last sequence update:	May 31, 2011
Last modified:	May 1, 2013
This is version 98 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program