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Reviewed, UniProtKB/Swiss-Prot Q9FV53 (DEF1A_ARATH)

Last modified February 9, 2010. Version 75. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Peptide deformylase 1A, chloroplastic
      Short name=PDF 1A
      Short name=AtPDF1A
      Short name=AtDEF1
    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) [Complete proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Arabidopsis

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Protein attributes

Sequence length259 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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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.5

Enzyme regulation

Inhibited by actinonin. Ref.5 Ref.4

Subunit structure

Homodimer. Ref.7

Subcellular location

Plastid › chloroplast stroma. Mitochondrion. Note: Reported by Ref.1 to be localized to mitochondria based on transient expression in an heterologous system. Ref.1 Ref.4

Tissue specificity

Expressed in roots, leaves, flowers and siliques. Ref.1

Disruption phenotype

No visible phenotype. Ref.6

Sequence similarities

Belongs to the polypeptide deformylase family.

Biophysicochemical properties

Kinetic parameters:

KM=240 µM for N-formyl-Met-Leu-rho-nitroanilide

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

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 5050Chloroplast Potential
Chain51 – 259209Peptide deformylase 1A, chloroplastic
PRO_0000006730

Regions

Region113 – 1164Substrate binding
Region181 – 1866Dimerization
Region226 – 24419Dimerization

Sites

Active site2211
Metal binding1781Zinc
Metal binding2201Zinc
Metal binding2241Zinc
Binding site1771Substrate; via carbonyl oxygen

Secondary structure

1 ............................. 259
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
Q9FV53-1 [UniParc].

Last modified December 5, 2001. Version 2.
Checksum: F524D19C9D21463D

FASTA25928,914
        10         20         30         40         50         60 
METLFRVSLR LLPVSAAVTC RSIRFPVSRP GSSHLLNRKL YNLPTSSSSS LSTKAGWLLG 

        70         80         90        100        110        120 
LGEKKKKVDL PEIVASGDPV LHEKAREVDP GEIGSERIQK IIDDMIKVMR LAPGVGLAAP 

       130        140        150        160        170        180 
QIGVPLRIIV LEDTKEYISY APKEEILAQE RRHFDLMVMV NPVLKERSNK KALFFEGCLS 

       190        200        210        220        230        240 
VDGFRAAVER YLEVVVTGYD RQGKRIEVNA SGWQARILQH ECDHLDGNLY VDKMVPRTFR 

       250 
TVDNLDLPLA EGCPKLGPQ

« Hide

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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: 11060042] [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: 11130712] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[3]"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: 14593172] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[4]"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: 11553738] [Abstract]
Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[5]"Distinctive features of the two classes of eukaryotic peptide deformylases."
Serero A., Giglione C., Meinnel T.
J. Mol. Biol. 314:695-708(2001) [PubMed: 11733990] [Abstract]
Cited for: COFACTOR, ENZYME REGULATION.
[6]"Control of protein life-span by N-terminal methionine excision."
Giglione C., Vallon O., Meinnel T.
EMBO J. 22:13-23(2003) [PubMed: 12505980] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
[7]"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: 16192279] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 69-257 IN COMPLEX WITH ZINC IONS AND SUBSTRATE, HOMODIMERIZATION.
+Additional computationally mapped references.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AF250959 mRNA. Translation: AAG33973.1. Different initiation.
AC007591 Genomic DNA. Translation: AAD39667.1.
AF361861 mRNA. Translation: AAK32873.1.
AY129485 mRNA. Translation: AAM91071.1.
IPIIPI00534874.
PIRE86288.
RefSeqNP_563974.1.
UniGeneAt.11423
At.19791
Rra.4371

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZXZX-ray2.80A/B69-257[»]
1ZY0X-ray2.90A/B69-257[»]
1ZY1X-ray3.00A/B69-257[»]
ModBaseSearch...

Protein-protein interaction databases

STRINGQ9FV53.

Proteomic databases

PRIDEQ9FV53.

Genome annotation databases

GeneID838109.
GenomeReviewsGene locus AT1G15390 in contig CT485782_GR.
KEGGath:AT1G15390.
NMPDRfig|3702.1.peg.1844.

Organism-specific databases

TAIRAt1g15390.

Phylogenomic databases

eggNOGKOG3137.
HOGENOMHBG665227.
InParanoidQ9FV53.

Enzyme and pathway databases

BRENDA3.5.1.88. 302.

Gene expression databases

ArrayExpressQ9FV53.
GenevestigatorQ9FV53.
GermOnlineAT1G15390. Arabidopsis thaliana.

Family and domain databases

InterProIPR000181. Fmet_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
PANTHERPTHR10458. Fmet_deformylase. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

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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: December 5, 2001
Last modified: February 9, 2010
This is version 75 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectPPAP (Plant Proteome Annotation Project)

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Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents