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Q9FV53

- DEF1A_ARATH

UniProt

Q9FV53 - DEF1A_ARATH

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Protein

Peptide deformylase 1A, chloroplastic/mitochondrial

Gene

PDF1A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Removes the formyl group from the N-terminal Met of newly synthesized proteins.1 Publication

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Cofactori

Binds 1 Zinc ion per subunit.1 Publication

Enzyme regulationi

Inhibited by actinonin.2 Publications

Kineticsi

  1. KM=240 µM for N-formyl-Met-Leu-rho-nitroanilide1 Publication
  2. KM=710 µM for N-formyl-Met-Ala-Ser1 Publication

Vmax=0.11 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide1 Publication

Vmax=0.20 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei187 – 1871Substrate; via carbonyl oxygen1 Publication
Metal bindingi188 – 1881Zinc
Metal bindingi230 – 2301Zinc
Active sitei231 – 2311
Metal bindingi234 – 2341Zinc

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: TAIR

GO - Biological processi

  1. co-translational protein modification Source: TAIR
  2. translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciARA:AT1G15390-MONOMER.
SABIO-RKQ9FV53.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1A, chloroplastic/mitochondrial (EC:3.5.1.88)
Short name:
AtDEF1
Short name:
AtPDF1A
Short name:
PDF 1A
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:PDF1A
Synonyms:DEF1
Ordered Locus Names:At1g15390
ORF Names:F9L1.34, F9L1_34
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 1

Organism-specific databases

TAIRiAT1G15390.

Subcellular locationi

Plastidchloroplast stroma. Mitochondrion
Note: Reported to be localized to mitochondria, based on transient GFP expression in a heterologous system (PubMed:11060042), but also shown to be imported and correctly processed in isolated chloroplast (PubMed:11553738).2 Publications

GO - Cellular componenti

  1. chloroplast Source: TAIR
  2. mitochondrion Source: TAIR
  3. plant-type cell wall Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid

Pathology & Biotechi

Disruption phenotypei

No visible phenotype.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6060Chloroplast and mitochondrionSequence AnalysisAdd
BLAST
Chaini61 – 269209Peptide deformylase 1A, chloroplastic/mitochondrialPRO_0000006730Add
BLAST

Proteomic databases

PaxDbiQ9FV53.
PRIDEiQ9FV53.

Expressioni

Tissue specificityi

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

Gene expression databases

GenevestigatoriQ9FV53.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi23349. 1 interaction.
STRINGi3702.AT1G15390.1-P.

Structurei

Secondary structure

1
269
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi89 – 913
Helixi100 – 1023
Helixi106 – 12116
Beta strandi125 – 1284
Helixi129 – 1324
Beta strandi138 – 1436
Helixi145 – 1484
Helixi153 – 1597
Beta strandi164 – 17916
Beta strandi181 – 1888
Beta strandi191 – 20919
Beta strandi215 – 2217
Helixi222 – 23514
Helixi240 – 2423
Helixi252 – 2543

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliQ9FV53.
SMRiQ9FV53. Positions 79-267.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9FV53.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni123 – 1264Substrate binding
Regioni191 – 1966Dimerization
Regioni236 – 25419DimerizationAdd
BLAST

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
InParanoidiQ9FV53.
KOiK01462.
OMAiHIDKENP.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9FV53-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGLHRDEATA METLFRVSLR LLPVSAAVTC RSIRFPVSRP GSSHLLNRKL
60 70 80 90 100
YNLPTSSSSS LSTKAGWLLG LGEKKKKVDL PEIVASGDPV LHEKAREVDP
110 120 130 140 150
GEIGSERIQK IIDDMIKVMR LAPGVGLAAP QIGVPLRIIV LEDTKEYISY
160 170 180 190 200
APKEEILAQE RRHFDLMVMV NPVLKERSNK KALFFEGCLS VDGFRAAVER
210 220 230 240 250
YLEVVVTGYD RQGKRIEVNA SGWQARILQH ECDHLDGNLY VDKMVPRTFR
260
TVDNLDLPLA EGCPKLGPQ
Length:269
Mass (Da):29,996
Last modified:May 31, 2011 - v3
Checksum:iBDDF13CC38F319C3
GO

Sequence cautioni

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 databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiE86288.
RefSeqiNP_563974.1. NM_101408.2.
UniGeneiAt.11423.
At.19791.

Genome annotation databases

EnsemblPlantsiAT1G15390.1; AT1G15390.1; AT1G15390.
GeneIDi838109.
KEGGiath:AT1G15390.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi E86288.
RefSeqi NP_563974.1. NM_101408.2.
UniGenei At.11423.
At.19791.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
4JE6 X-ray 2.00 A/B 79-267 [» ]
4JE7 X-ray 2.10 A/B 79-267 [» ]
4JE8 X-ray 2.40 A/B 79-267 [» ]
ProteinModelPortali Q9FV53.
SMRi Q9FV53. Positions 79-267.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 23349. 1 interaction.
STRINGi 3702.AT1G15390.1-P.

Chemistry

ChEMBLi CHEMBL1075041.

Proteomic databases

PaxDbi Q9FV53.
PRIDEi Q9FV53.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT1G15390.1 ; AT1G15390.1 ; AT1G15390 .
GeneIDi 838109.
KEGGi ath:AT1G15390.

Organism-specific databases

TAIRi AT1G15390.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243508.
InParanoidi Q9FV53.
KOi K01462.
OMAi HIDKENP.

Enzyme and pathway databases

BioCyci ARA:AT1G15390-MONOMER.
SABIO-RK Q9FV53.

Miscellaneous databases

EvolutionaryTracei Q9FV53.
PROi Q9FV53.

Gene expression databases

Genevestigatori Q9FV53.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiDEF1A_ARATH
AccessioniPrimary (citable) accession number: Q9FV53
Secondary accession number(s): Q9XI30
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: May 31, 2011
Last modified: October 29, 2014
This is version 109 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3