Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q5VNN5 (DEF1B_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 63. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptide deformylase 1B, chloroplastic

Short name=OsPDF1B
Short name=PDF 1B
EC=3.5.1.88
Gene names
Name:PDF1B
Ordered Locus Names:Os01g0637600, LOC_Os01g45070
ORF Names:OsJ_002667, OsJ_02762, P0004A09.6, P0696E01.27
OrganismOryza sativa subsp. japonica (Rice) [Reference proteome]
Taxonomic identifier39947 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza

Protein attributes

Sequence length269 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

Removes the formyl group from the N-terminal Met of newly synthesized proteins. HAMAP-Rule MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP-Rule MF_00163

Enzyme regulation

Inhibited by actinonin. HAMAP-Rule MF_00163

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_00163

Subcellular location

Plastidchloroplast stroma. Mitochondrion Ref.1.

Tissue specificity

Mainly expressed in mature leaves and sheaths. Ref.1

Disruption phenotype

Chlorina and retarded growth. Ref.1

Sequence similarities

Belongs to the polypeptide deformylase family.

Sequence caution

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

Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentChloroplast
Mitochondrion
Plastid
   DomainTransit peptide
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentchloroplast stroma

Inferred from electronic annotation. Source: UniProtKB-SubCell

mitochondrion

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 5151Chloroplast Potential
Chain52 – 269218Peptide deformylase 1B, chloroplastic HAMAP-Rule MF_00163
PRO_0000369421

Sites

Active site2111 By similarity
Metal binding1681Iron By similarity
Metal binding2101Iron By similarity
Metal binding2141Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5VNN5 [UniParc].

Last modified December 7, 2004. Version 1.
Checksum: 0E4ED8966241BFF5

FASTA26929,676
        10         20         30         40         50         60 
MAARLHLRLG PRLRGFASSF APLLAAHPRA LPLSRMGSVA PLAAARARRG FGSAVATAPP 

        70         80         90        100        110        120 
AEDEDFATAA DLQFEPPLKV VKYPDPILRA RNKRINTFDD NLRSLTDEMF DVMYKTDGIG 

       130        140        150        160        170        180 
LSAPQVGVNV QLMVFNPAGV KGEGEEIVLV NPVVYKMSKR LLVYEEGCLS FPGIYANVVR 

       190        200        210        220        230        240 
PDNVKIDAQD VTGAKIKVKL SGLSARVFQH EFDHLQGILF FDRMSLDVLE SVREGLKDLE 

       250        260 
KKYEESTGLV SPESIENYKG RKDLISFSR 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The map-based sequence of the rice genome."
International rice genome sequencing project (IRGSP)
Nature 436:793-800(2005) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001043669.1. NM_001050204.1.
UniGeneOs.27933.

3D structure databases

ProteinModelPortalQ5VNN5.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING39947.LOC_Os01g45070.1.

Proteomic databases

PRIDEQ5VNN5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsOS01T0637600-01; OS01T0637600-01; OS01G0637600.
GeneID4326576.
KEGGosa:4326576.

Organism-specific databases

GrameneQ5VNN5.

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAFFDRMTE.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF1B_ORYSJ
AccessionPrimary (citable) accession number: Q5VNN5
Secondary accession number(s): A2ZVU5, B9EY95
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: December 7, 2004
Last modified: May 14, 2014
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations