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Protein

Peptide deformylase 1A, chloroplastic

Gene

PDF1A

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

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 keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei178Substrate; via carbonyl oxygenBy similarity1
Metal bindingi179ZincBy similarity1
Metal bindingi221ZincBy similarity1
Active sitei222By similarity1
Metal bindingi225ZincBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandMetal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.5.1.88 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
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
Proteomesi
  • UP000059680 Componenti: Chromosome 1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 43ChloroplastSequence analysisAdd BLAST43
ChainiPRO_000036942044 – 260Peptide deformylase 1A, chloroplasticAdd BLAST217

Proteomic databases

PaxDbiB6RGY0

Expressioni

Tissue specificityi

Mainly expressed in roots. Lower expression in shoots, mature panicles at flowering stages and mature leaves.1 Publication

Gene expression databases

ExpressionAtlasiB6RGY0 differential
GenevisibleiB6RGY0 OS

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi39947.LOC_Os01g37510.1

Structurei

3D structure databases

ProteinModelPortaliB6RGY0
SMRiB6RGY0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni114 – 117Substrate bindingBy similarity4
Regioni182 – 187DimerizationBy similarity6
Regioni227 – 245DimerizationBy similarityAdd BLAST19

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi47 – 50Poly-Gly4
Compositional biasi57 – 63Poly-Gly7

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG3137 Eukaryota
COG0242 LUCA
InParanoidiB6RGY0
KOiK01462
OrthoDBiEOG09360MKH

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
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.

B6RGY0-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:260
Mass (Da):27,493
Last modified:December 16, 2008 - v1
Checksum:iA0CEB3C83E884CCE
GO

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.
RefSeqiXP_015621038.1, XM_015765552.1
UniGeneiOs.14593

Genome annotation databases

EnsemblPlantsiOs01t0555800-01; Os01t0555800-01; Os01g0555800
GeneIDi4324565
GrameneiOs01t0555800-01; Os01t0555800-01; Os01g0555800
KEGGiosa:4324565

Similar proteinsi

Entry informationi

Entry nameiDEF1A_ORYSJ
AccessioniPrimary (citable) accession number: B6RGY0
Secondary accession number(s): A2ZUB7, B9EXI6, Q0JLZ1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: December 16, 2008
Last modified: May 23, 2018
This is version 63 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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