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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)DescriptionActionsGraphical viewLength
Metal bindingi168IronBy similarity1
Metal bindingi210IronBy similarity1
Active sitei211By similarity1
Metal bindingi214IronBy similarity1

GO - Molecular functioni

GO - Biological processi

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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chromosome 1

Subcellular locationi

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Transit peptidei1 – 51ChloroplastSequence analysisAdd BLAST51
ChainiPRO_000036942152 – 269Peptide deformylase 1B, chloroplasticAdd BLAST218

Proteomic databases

PaxDbiQ5VNN5.
PRIDEiQ5VNN5.

Expressioni

Tissue specificityi

Mainly expressed in mature leaves and sheaths.1 Publication

Gene expression databases

GenevisibleiQ5VNN5. OS.

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

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
HOGENOMiHOG000243509.
InParanoidiQ5VNN5.
KOiK01462.
OMAiAVCNCFL.
OrthoDBiEOG09360NFS.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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 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.
AP014957 Genomic DNA. Translation: BAS73349.1.
CM000138 Genomic DNA. Translation: EEE55058.1. Sequence problems.
AK106980 mRNA. Translation: BAG97903.1.
RefSeqiXP_015612309.1. XM_015756823.1.
UniGeneiOs.27933.

Genome annotation databases

EnsemblPlantsiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
GeneIDi4326576.
GrameneiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
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.
AP014957 Genomic DNA. Translation: BAS73349.1.
CM000138 Genomic DNA. Translation: EEE55058.1. Sequence problems.
AK106980 mRNA. Translation: BAG97903.1.
RefSeqiXP_015612309.1. XM_015756823.1.
UniGeneiOs.27933.

3D structure databases

ProteinModelPortaliQ5VNN5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os01g45070.1.

Proteomic databases

PaxDbiQ5VNN5.
PRIDEiQ5VNN5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
GeneIDi4326576.
GrameneiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
KEGGiosa:4326576.

Phylogenomic databases

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
HOGENOMiHOG000243509.
InParanoidiQ5VNN5.
KOiK01462.
OMAiAVCNCFL.
OrthoDBiEOG09360NFS.

Enzyme and pathway databases

BRENDAi3.5.1.88. 4460.

Gene expression databases

GenevisibleiQ5VNN5. OS.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

Entry informationi

Entry nameiDEF1B_ORYSJ
AccessioniPrimary (citable) accession number: Q5VNN5
Secondary accession number(s): A0A0P0V5R4, A2ZVU5, B9EY95
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: December 7, 2004
Last modified: November 30, 2016
This is version 77 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

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 one 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.