Reviewed,
UniProtKB/Swiss-Prot Q9FV53 (DEF1A_ARATH)
Last modified
February 9, 2010.
Version 75.
History...
Clusters with 100%,
90%,
50% identity |
Documents (3) |
Third-party data |
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Names and origin
| Protein names | Recommended 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 |
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| Organism | Arabidopsis thaliana (Mouse-ear cress) [Complete proteome] | ||||||||
| Taxonomic identifier | 3702 [NCBI] | ||||||||
| Taxonomic lineage | Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Arabidopsis |
Protein attributes
| Sequence length | 259 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.5 |
| Enzyme regulation | |
| 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 |
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 |
| Gene Ontology (GO) | |
| Biological process | co-translational protein modification Ref.5 Inferred from direct assay. Source: TAIR translationInferred from electronic annotation. Source: UniProtKB-KW |
| Cellular component | chloroplast stroma Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Ref.1Inferred from direct assay. Source: TAIR plant-type cell wallInferred from direct assay. Source: TAIR |
| Molecular function | iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Ref.5Inferred from direct assay. Source: TAIR zinc ion bindingInferred from electronic annotation. Source: UniProtKB-KW |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Transit peptide | 1 – 50 | 50 | Chloroplast Potential | ||||||||||||||||||||||||||||||||||
| Chain | 51 – 259 | 209 | Peptide deformylase 1A, chloroplastic | PRO_0000006730 | |||||||||||||||||||||||||||||||||
Regions | |||||||||||||||||||||||||||||||||||||
| Region | 113 – 116 | 4 | Substrate binding | ||||||||||||||||||||||||||||||||||
| Region | 181 – 186 | 6 | Dimerization | ||||||||||||||||||||||||||||||||||
| Region | 226 – 244 | 19 | Dimerization | ||||||||||||||||||||||||||||||||||
Sites | |||||||||||||||||||||||||||||||||||||
| Active site | 221 | 1 | |||||||||||||||||||||||||||||||||||
| Metal binding | 178 | 1 | Zinc | ||||||||||||||||||||||||||||||||||
| Metal binding | 220 | 1 | Zinc | ||||||||||||||||||||||||||||||||||
| Metal binding | 224 | 1 | Zinc | ||||||||||||||||||||||||||||||||||
| Binding site | 177 | 1 | Substrate; via carbonyl oxygen | ||||||||||||||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||||||||||||
| Helix | 79 – 81 | 3 | |||||||||||||||||||||||||||||||||||
| Turn | 90 – 94 | 5 | |||||||||||||||||||||||||||||||||||
| Helix | 96 – 111 | 16 | |||||||||||||||||||||||||||||||||||
| Beta strand | 115 – 118 | 4 | |||||||||||||||||||||||||||||||||||
| Helix | 119 – 122 | 4 | |||||||||||||||||||||||||||||||||||
| Beta strand | 126 – 133 | 8 | |||||||||||||||||||||||||||||||||||
| Helix | 135 – 139 | 5 | |||||||||||||||||||||||||||||||||||
| Helix | 143 – 148 | 6 | |||||||||||||||||||||||||||||||||||
| Beta strand | 154 – 169 | 16 | |||||||||||||||||||||||||||||||||||
| Beta strand | 171 – 178 | 8 | |||||||||||||||||||||||||||||||||||
| Beta strand | 181 – 199 | 19 | |||||||||||||||||||||||||||||||||||
| Beta strand | 205 – 211 | 7 | |||||||||||||||||||||||||||||||||||
| Helix | 212 – 225 | 14 | |||||||||||||||||||||||||||||||||||
| Helix | 230 – 232 | 3 | |||||||||||||||||||||||||||||||||||
| Helix | 242 – 244 | 3 | |||||||||||||||||||||||||||||||||||
Sequences
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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. 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. 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. |
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. | ||||||||||||||||||||||||
| IPI | IPI00534874. | ||||||||||||||||||||||||
| PIR | E86288. | ||||||||||||||||||||||||
| RefSeq | NP_563974.1. | ||||||||||||||||||||||||
| UniGene | At.11423 At.19791 Rra.4371 | ||||||||||||||||||||||||
3D structure databases | |||||||||||||||||||||||||
| PDBe RCSB PDB PDBj |
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| ModBase | Search... | ||||||||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||||||||
| STRING | Q9FV53. | ||||||||||||||||||||||||
Proteomic databases | |||||||||||||||||||||||||
| PRIDE | Q9FV53. | ||||||||||||||||||||||||
Genome annotation databases | |||||||||||||||||||||||||
| GeneID | 838109. | ||||||||||||||||||||||||
| GenomeReviews | Gene locus AT1G15390 in contig CT485782_GR. | ||||||||||||||||||||||||
| KEGG | ath:AT1G15390. | ||||||||||||||||||||||||
| NMPDR | fig|3702.1.peg.1844. | ||||||||||||||||||||||||
Organism-specific databases | |||||||||||||||||||||||||
| TAIR | At1g15390. | ||||||||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||||||||
| eggNOG | KOG3137. | ||||||||||||||||||||||||
| HOGENOM | HBG665227. | ||||||||||||||||||||||||
| InParanoid | Q9FV53. | ||||||||||||||||||||||||
Enzyme and pathway databases | |||||||||||||||||||||||||
| BRENDA | 3.5.1.88. 302. | ||||||||||||||||||||||||
Gene expression databases | |||||||||||||||||||||||||
| ArrayExpress | Q9FV53. | ||||||||||||||||||||||||
| Genevestigator | Q9FV53. | ||||||||||||||||||||||||
| GermOnline | AT1G15390. Arabidopsis thaliana. | ||||||||||||||||||||||||
Family and domain databases | |||||||||||||||||||||||||
| InterPro | IPR000181. Fmet_deformylase. [Graphical view] | ||||||||||||||||||||||||
| Gene3D | G3DSA:3.90.45.10. Fmet_deformylase. 1 hit. | ||||||||||||||||||||||||
| PANTHER | PTHR10458. Fmet_deformylase. 1 hit. | ||||||||||||||||||||||||
| Pfam | PF01327. Pep_deformylase. 1 hit. [Graphical view] | ||||||||||||||||||||||||
| PRINTS | PR01576. PDEFORMYLASE. | ||||||||||||||||||||||||
| TIGRFAMs | TIGR00079. pept_deformyl. 1 hit. | ||||||||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||||||||
Entry information
| Entry name | DEF1A_ARATH | ||||||||
| Accession | Primary (citable) accession number: Q9FV53 Secondary accession number(s): Q9XI30 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | PPAP (Plant Proteome Annotation Project) | ||||||||
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 |

Clusters with


