UniProtKB - B6RGY0 (DEF1A_ORYSJ)
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Protein
Peptide deformylase 1A, chloroplastic
Gene
PDF1A
Organism
Oryza sativa subsp. japonica (Rice)
Status
Functioni
Removes the formyl group from the N-terminal Met of newly synthesized proteins.
Catalytic activityi
Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
Cofactori
Zn2+By similarityNote: Binds 1 Zn2+ ion per subunit.By similarity
Enzyme regulationi
Inhibited by actinonin.
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 178 | Substrate; via carbonyl oxygenBy similarity | 1 | |
Metal bindingi | 179 | ZincBy similarity | 1 | |
Metal bindingi | 221 | ZincBy similarity | 1 | |
Active sitei | 222 | By similarity | 1 | |
Metal bindingi | 225 | ZincBy similarity | 1 |
GO - Molecular functioni
- metal ion binding Source: UniProtKB-KW
- peptide deformylase activity Source: GO_Central
GO - Biological processi
- co-translational protein modification Source: GO_Central
- N-terminal protein amino acid modification Source: GO_Central
- peptidyl-methionine modification Source: GO_Central
- translation Source: UniProtKB-KW
Keywordsi
Molecular function | Hydrolase |
Biological process | Protein biosynthesis |
Ligand | Metal-binding, Zinc |
Enzyme and pathway databases
BRENDAi | 3.5.1.88. 4460. |
Names & Taxonomyi
Protein namesi | Recommended name: Peptide deformylase 1A, chloroplastic (EC:3.5.1.88)Short name: OsPDF1A Short name: PDF 1A |
Gene namesi | Name:PDF1A Ordered Locus Names:Os01g0555800, LOC_Os01g37510 ORF Names:OsJ_002139, OsJ_02204 |
Organismi | Oryza sativa subsp. japonica (Rice) |
Taxonomic identifieri | 39947 [NCBI] |
Taxonomic lineagei | Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BOP clade › Oryzoideae › Oryzeae › Oryzinae › Oryza › Oryza sativa |
Proteomesi |
|
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Transit peptidei | 1 – 43 | ChloroplastSequence analysisAdd BLAST | 43 | |
ChainiPRO_0000369420 | 44 – 260 | Peptide deformylase 1A, chloroplasticAdd BLAST | 217 |
Proteomic databases
PaxDbi | B6RGY0. |
PRIDEi | B6RGY0. |
Expressioni
Tissue specificityi
Mainly expressed in roots. Lower expression in shoots, mature panicles at flowering stages and mature leaves.1 Publication
Gene expression databases
ExpressionAtlasi | B6RGY0. baseline and differential. |
Genevisiblei | B6RGY0. OS. |
Interactioni
Subunit structurei
Homodimer.By similarity
Protein-protein interaction databases
STRINGi | 39947.LOC_Os01g37510.1. |
Structurei
3D structure databases
ProteinModelPortali | B6RGY0. |
SMRi | B6RGY0. |
ModBasei | Search... |
MobiDBi | Search... |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 114 – 117 | Substrate bindingBy similarity | 4 | |
Regioni | 182 – 187 | DimerizationBy similarity | 6 | |
Regioni | 227 – 245 | DimerizationBy similarityAdd BLAST | 19 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 47 – 50 | Poly-Gly | 4 | |
Compositional biasi | 57 – 63 | Poly-Gly | 7 |
Sequence similaritiesi
Belongs to the polypeptide deformylase family.Curated
Keywords - Domaini
Transit peptidePhylogenomic databases
eggNOGi | KOG3137. Eukaryota. COG0242. LUCA. |
InParanoidi | B6RGY0. |
KOi | K01462. |
OrthoDBi | EOG09360MKH. |
Family and domain databases
CDDi | cd00487. Pep_deformylase. 1 hit. |
Gene3Di | 3.90.45.10. 1 hit. |
HAMAPi | MF_00163. Pep_deformylase. 1 hit. |
InterProi | View protein in InterPro IPR023635. Peptide_deformylase. IPR036821. Peptide_deformylase_sf. |
PANTHERi | PTHR10458. PTHR10458. 1 hit. |
Pfami | View protein in Pfam PF01327. Pep_deformylase. 1 hit. |
PRINTSi | PR01576. PDEFORMYLASE. |
SUPFAMi | SSF56420. SSF56420. 1 hit. |
TIGRFAMsi | TIGR00079. pept_deformyl. 1 hit. |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
B6RGY0-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MEAHLRPLSA AALLLSPAAP LPTAVAASAR RASPGGRRWS SVRASAGGGG
60 70 80 90 100
WLSGLLGGKG GGGAPTAMTV TPGTVKAGDP VLHEPAQDVA PGDIPSEKVQ
110 120 130 140 150
GVIDRMVAVM RKAPGVGLAA PQIGVPLKII VLEDTQEYIS YAPKKDIEAQ
160 170 180 190 200
DRRPFDLLVI INPKLKTTSK RTALFFEGCL SVDGYRALVE RHLDVEVSGL
210 220 230 240 250
DRNGRPIKVE ASGWQARILQ HECDHLEGTL YVDTMVPRTF RIVDNLDLPL
260
PVGCPPIGAR
Sequence cautioni
The sequence BAF05237 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence EEE54799 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | EU213045 mRNA. Translation: ABY64739.1. AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems. AP014957 Genomic DNA. No translation available. CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation. |
RefSeqi | XP_015621038.1. XM_015765552.1. |
UniGenei | Os.14593. |
Genome annotation databases
EnsemblPlantsi | Os01t0555800-01; Os01t0555800-01; Os01g0555800. |
GeneIDi | 4324565. |
Gramenei | Os01t0555800-01; Os01t0555800-01; Os01g0555800. |
KEGGi | osa:4324565. |
Similar proteinsi
Entry informationi
Entry namei | DEF1A_ORYSJ | |
Accessioni | B6RGY0Primary (citable) accession number: B6RGY0 Secondary accession number(s): A2ZUB7, B9EXI6, Q0JLZ1 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | April 14, 2009 |
Last sequence update: | December 16, 2008 | |
Last modified: | February 28, 2018 | |
This is version 62 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Plant Protein Annotation Program |