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Protein

Peptide deformylase 1B, chloroplastic

Gene

PDF1B

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

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Enzyme regulationi

Inhibited by actinonin.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi168 – 1681IronBy similarity
Metal bindingi210 – 2101IronBy similarity
Active sitei211 – 2111By similarity
Metal bindingi214 – 2141IronBy similarity

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-EC

GO - Biological processi

  1. translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BRENDAi3.5.1.88. 4460.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1B, chloroplastic (EC:3.5.1.88)
Short name:
OsPDF1B
Short name:
PDF 1B
Gene namesi
Name:PDF1B
Ordered Locus Names:Os01g0637600, LOC_Os01g45070
ORF Names:OsJ_002667, OsJ_02762, P0004A09.6, P0696E01.27
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000000763 Componenti: Chromosome 1

Organism-specific databases

GrameneiQ5VNN5.

Subcellular locationi

  1. Plastidchloroplast stroma 1 Publication
  2. Mitochondrion 1 Publication

GO - Cellular componenti

  1. chloroplast stroma Source: UniProtKB-SubCell
  2. mitochondrion Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid

Pathology & Biotechi

Disruption phenotypei

Chlorina and retarded growth.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 5151ChloroplastSequence AnalysisAdd
BLAST
Chaini52 – 269218Peptide deformylase 1B, chloroplasticPRO_0000369421Add
BLAST

Proteomic databases

PRIDEiQ5VNN5.

Expressioni

Tissue specificityi

Mainly expressed in mature leaves and sheaths.1 Publication

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi39947.LOC_Os01g45070.1.

Structurei

3D structure databases

ProteinModelPortaliQ5VNN5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiQ5VNN5.
KOiK01462.
OMAiVMYNINE.

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.

Q5VNN5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAARLHLRLG PRLRGFASSF APLLAAHPRA LPLSRMGSVA PLAAARARRG
60 70 80 90 100
FGSAVATAPP AEDEDFATAA DLQFEPPLKV VKYPDPILRA RNKRINTFDD
110 120 130 140 150
NLRSLTDEMF DVMYKTDGIG LSAPQVGVNV QLMVFNPAGV KGEGEEIVLV
160 170 180 190 200
NPVVYKMSKR LLVYEEGCLS FPGIYANVVR PDNVKIDAQD VTGAKIKVKL
210 220 230 240 250
SGLSARVFQH EFDHLQGILF FDRMSLDVLE SVREGLKDLE KKYEESTGLV
260
SPESIENYKG RKDLISFSR
Length:269
Mass (Da):29,676
Last modified:December 7, 2004 - v1
Checksum:i0E4ED8966241BFF5
GO

Sequence cautioni

The sequence EEE55058.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU213046 mRNA. Translation: ABY64740.1.
AP003607 Genomic DNA. Translation: BAD68576.1.
AP004367 Genomic DNA. Translation: BAD68940.1.
AP008207 Genomic DNA. Translation: BAF05583.1.
CM000138 Genomic DNA. Translation: EEE55058.1. Sequence problems.
AK106980 mRNA. Translation: BAG97903.1.
RefSeqiNP_001043669.1. NM_001050204.1.
UniGeneiOs.27933.

Genome annotation databases

EnsemblPlantsiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
GeneIDi4326576.
KEGGiosa:4326576.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU213046 mRNA. Translation: ABY64740.1.
AP003607 Genomic DNA. Translation: BAD68576.1.
AP004367 Genomic DNA. Translation: BAD68940.1.
AP008207 Genomic DNA. Translation: BAF05583.1.
CM000138 Genomic DNA. Translation: EEE55058.1. Sequence problems.
AK106980 mRNA. Translation: BAG97903.1.
RefSeqiNP_001043669.1. NM_001050204.1.
UniGeneiOs.27933.

3D structure databases

ProteinModelPortaliQ5VNN5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os01g45070.1.

Proteomic databases

PRIDEiQ5VNN5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
GeneIDi4326576.
KEGGiosa:4326576.

Organism-specific databases

GrameneiQ5VNN5.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiQ5VNN5.
KOiK01462.
OMAiVMYNINE.

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, DISRUPTION PHENOTYPE.
    Strain: cv. Dongjin.
  2. "The genome sequence and structure of rice chromosome 1."
    Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H., Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.
    , Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M., Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S., Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H., Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S., Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y., Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S., Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H., Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.
    Nature 420:312-316(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  4. "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.
  5. "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.
  6. "Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice."
    The rice full-length cDNA consortium
    Science 301:376-379(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiDEF1B_ORYSJ
AccessioniPrimary (citable) accession number: Q5VNN5
Secondary accession number(s): A2ZVU5, B9EY95
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: December 7, 2004
Last modified: April 1, 2015
This is version 68 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.