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Q9FV53 (DEF1A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length269 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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. HAMAP-Rule MF_00163

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

Plastidchloroplast 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 6060Chloroplast and mitochondrion Potential
Chain61 – 269209Peptide deformylase 1A, chloroplastic/mitochondrial HAMAP-Rule MF_00163
PRO_0000006730

Regions

Region123 – 1264Substrate binding HAMAP-Rule MF_00163
Region191 – 1966Dimerization HAMAP-Rule MF_00163
Region236 – 25419Dimerization HAMAP-Rule MF_00163

Sites

Active site2311
Metal binding1881Zinc
Metal binding2301Zinc
Metal binding2341Zinc
Binding site1871Substrate; via carbonyl oxygen

Secondary structure

............................. 269
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9FV53 [UniParc].

Last modified May 31, 2011. Version 3.
Checksum: BDDF13CC38F319C3

FASTA26929,996
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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. expand/collapse author list , 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.
PIRE86288.
RefSeqNP_563974.1. NM_101408.2.
UniGeneAt.11423.
At.19791.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZXZX-ray2.80A/B79-267[»]
1ZY0X-ray2.90A/B79-267[»]
1ZY1X-ray3.00A/B79-267[»]
4JE6X-ray2.00A/B79-267[»]
4JE7X-ray2.10A/B79-267[»]
4JE8X-ray2.40A/B79-267[»]
ProteinModelPortalQ9FV53.
SMRQ9FV53. Positions 79-267.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid23349. 1 interaction.
STRING3702.AT1G15390.1-P.

Chemistry

ChEMBLCHEMBL1075041.

Proteomic databases

PaxDbQ9FV53.
PRIDEQ9FV53.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G15390.1; AT1G15390.1; AT1G15390.
GeneID838109.
KEGGath:AT1G15390.

Organism-specific databases

TAIRAT1G15390.

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243508.
InParanoidQ9FV53.
KOK01462.
OMAHIDKENP.

Enzyme and pathway databases

BioCycARA:AT1G15390-MONOMER.
SABIO-RKQ9FV53.

Gene expression databases

GenevestigatorQ9FV53.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9FV53.
PROQ9FV53.

Entry information

Entry nameDEF1A_ARATH
AccessionPrimary (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: June 11, 2014
This is version 107 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names