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Protein

Peptide deformylase 1A, chloroplastic

Gene

PDF1A

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei178 – 1781Substrate; via carbonyl oxygenBy similarity
Metal bindingi179 – 1791ZincBy similarity
Metal bindingi221 – 2211ZincBy similarity
Active sitei222 – 2221By similarity
Metal bindingi225 – 2251ZincBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Metal-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 cladeOryzoideaeOryzeaeOryzinaeOryza
ProteomesiUP000000763 Componenti: Chromosome 1

Organism-specific databases

GrameneiB6RGY0.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4343ChloroplastSequence AnalysisAdd
BLAST
Chaini44 – 260217Peptide deformylase 1A, chloroplasticPRO_0000369420Add
BLAST

Expressioni

Tissue specificityi

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

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi39947.LOC_Os01g37510.1.

Structurei

3D structure databases

ProteinModelPortaliB6RGY0.
SMRiB6RGY0. Positions 72-259.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni114 – 1174Substrate bindingBy similarity
Regioni182 – 1876DimerizationBy similarity
Regioni227 – 24519DimerizationBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi47 – 504Poly-Gly
Compositional biasi57 – 637Poly-Gly

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0242.
InParanoidiB6RGY0.
KOiK01462.
OMAiTFTNIHW.

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.

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 BAF05237.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence EEE54799.1 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.
CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation.
RefSeqiNP_001043323.1. NM_001049858.1.
UniGeneiOs.14593.

Genome annotation databases

GeneIDi4324565.
KEGGiosa:4324565.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU213045 mRNA. Translation: ABY64739.1.
AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems.
CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation.
RefSeqiNP_001043323.1. NM_001049858.1.
UniGeneiOs.14593.

3D structure databases

ProteinModelPortaliB6RGY0.
SMRiB6RGY0. Positions 72-259.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os01g37510.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi4324565.
KEGGiosa:4324565.

Organism-specific databases

GrameneiB6RGY0.

Phylogenomic databases

eggNOGiCOG0242.
InParanoidiB6RGY0.
KOiK01462.
OMAiTFTNIHW.

Enzyme and pathway databases

BRENDAi3.5.1.88. 4460.

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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Rice peptide deformylase PDF1B is crucial for development of chloroplasts."
    Moon S., Giglione C., Lee D.-Y., An S., Jeong D.-H., Meinnel T., An G.
    Plant Cell Physiol. 49:1536-1546(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    Strain: cv. Dongjin.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  3. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  4. "The genomes of Oryza sativa: a history of duplications."
    Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
    , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
    PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiDEF1A_ORYSJ
AccessioniPrimary (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: June 24, 2015
This is version 42 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.