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Q9FUZ2 (DEF1B_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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/mitochondrial

Short name=AtDEF2
Short name=AtPDF1B
Short name=PDF 1B
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:PDF1B
Synonyms:DEF2
Ordered Locus Names:At5g14660
ORF Names:T15N1_150
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length273 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide. Ref.1

Catalytic activity

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

Cofactor

Binds 1 Fe2+ ion. Ref.7

Enzyme regulation

Inhibited by actinonin. Ref.6 Ref.7

Subunit structure

Homodimer. Ref.9

Subcellular location

Plastidchloroplast stroma. Mitochondrion. Note: Reported to be localized to chloroplast and mitochondria based on transient GFP expression in a heterologous system (Ref.1). Ref.1 Ref.6

Tissue specificity

Expressed in leaves and flowers. Ref.1

Disruption phenotype

Albino. Ref.8

Sequence similarities

Belongs to the polypeptide deformylase family.

Biophysicochemical properties

Kinetic parameters:

KM=130 µM for N-formyl-Met-Leu-rho-nitroanilide Ref.6

KM=3200 µM for N-formyl-Met-Ala-Ser

Vmax=20 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide

Vmax=1.3 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser

Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentChloroplast
Mitochondrion
Plastid
   DomainTransit peptide
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentchloroplast

Inferred from direct assay PubMed 18431481. Source: TAIR

chloroplast 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 direct assay Ref.9. Source: TAIR

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 5656Chloroplast and mitochondrion Potential
Chain57 – 273217Peptide deformylase 1B, chloroplastic/mitochondrial HAMAP-Rule MF_00163
PRO_0000006732

Sites

Active site2141 By similarity
Metal binding1711Iron
Metal binding2131Iron
Metal binding2171Iron

Experimental info

Mutagenesis1781Y → A: Decrease in substrate affinity. Ref.9
Mutagenesis1781Y → F or R: Increase in substrate affinity. Ref.9
Sequence conflict481T → N in AAM62644. Ref.5
Sequence conflict2051R → S in AAG33980. Ref.1

Secondary structure

................................ 273
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9FUZ2 [UniParc].

Last modified December 15, 2003. Version 2.
Checksum: 25CDA90ED6D9603E

FASTA27330,610
        10         20         30         40         50         60 
MAVCNCFLQA PPLSRILLPV LSRRATTLSA GYGRLKSTVT FCSTVNRTSP LTSSVRAEVK 

        70         80         90        100        110        120 
RVSRKDDKVA SATDVQFETP LKIVEYPDPI LRAKNKRIDI FDENLKNLVD AMFDVMYKTD 

       130        140        150        160        170        180 
GIGLSAPQVG LNVQLMVFNP AGEPGEGKEI VLVNPKIKKY SDKLVPFDEG CLSFPGIYAE 

       190        200        210        220        230        240 
VVRPQSVKID ARDITGERFS ISLSRLPARI FQHEYDHLEG VLFFDRMTDQ VLDSIREELE 

       250        260        270 
ALEKKYEEKT GLPSPERVEA RQKRKAGVGF GKR 

« Hide

References

« Hide 'large scale' references
[1]"Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms."
Giglione C., Serero A., Pierre M., Boisson B., Meinnel T.
EMBO J. 19:5916-5929(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[2]"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. expand/collapse author list , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[3]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[4]"Empirical analysis of transcriptional activity in the Arabidopsis genome."
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. expand/collapse author list , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[5]"Full-length cDNA from Arabidopsis thaliana."
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]"Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis."
Dirk L.M., Williams M.A., Houtz R.L.
Plant Physiol. 127:97-107(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[7]"Distinctive features of the two classes of eukaryotic peptide deformylases."
Serero A., Giglione C., Meinnel T.
J. Mol. Biol. 314:695-708(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: COFACTOR, ENZYME REGULATION.
[8]"Control of protein life-span by N-terminal methionine excision."
Giglione C., Vallon O., Meinnel T.
EMBO J. 22:13-23(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
[9]"Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture."
Dirk L.M., Schmidt J.J., Cai Y., Barnes J.C., Hanger K.M., Nayak N.R., Williams M.A., Grossman R.B., Houtz R.L., Rodgers D.W.
Biochem. J. 413:417-427(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 65-257, HOMODIMERIZATION, MUTAGENESIS OF TYR-178.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF269165 mRNA. Translation: AAG33980.1.
AL163792 Genomic DNA. Translation: CAB87633.1.
CP002688 Genomic DNA. Translation: AED92059.1.
CP002688 Genomic DNA. Translation: AED92060.1.
AY050879 mRNA. Translation: AAK92816.1.
AY096673 mRNA. Translation: AAM20307.1.
AY085417 mRNA. Translation: AAM62644.1.
PIRT48639.
RefSeqNP_196970.1. NM_121470.3.
NP_850821.1. NM_180490.1.
UniGeneAt.5087.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3CPMX-ray2.40A65-257[»]
3M6OX-ray2.00A/B83-273[»]
3M6PX-ray2.00A/B83-273[»]
3M6QX-ray2.40A83-273[»]
3M6RX-ray2.40A/B/C/D83-273[»]
3O3JX-ray3.00A83-273[»]
3PN2X-ray2.00A83-273[»]
3PN3X-ray1.30A/B83-273[»]
3PN4X-ray1.90A83-273[»]
3PN5X-ray2.30A83-273[»]
3PN6X-ray2.10A/B83-273[»]
ProteinModelPortalQ9FUZ2.
SMRQ9FUZ2. Positions 74-257.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid16595. 3 interactions.
IntActQ9FUZ2. 2 interactions.

Proteomic databases

PaxDbQ9FUZ2.
PRIDEQ9FUZ2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G14660.1; AT5G14660.1; AT5G14660.
AT5G14660.2; AT5G14660.2; AT5G14660.
GeneID831318.
KEGGath:AT5G14660.

Organism-specific databases

TAIRAT5G14660.

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
InParanoidQ9FUZ2.
KOK01462.
OMADAKLHQQ.
PhylomeDBQ9FUZ2.
ProtClustDBCLSN2687238.

Enzyme and pathway databases

BioCycARA:AT5G14660-MONOMER.
ARA:GQT-2354-MONOMER.
SABIO-RKQ9FUZ2.

Gene expression databases

GenevestigatorQ9FUZ2.

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...

Other

EvolutionaryTraceQ9FUZ2.

Entry information

Entry nameDEF1B_ARATH
AccessionPrimary (citable) accession number: Q9FUZ2
Secondary accession number(s): Q8LEH0, Q949U8, Q9LYJ4
Entry history
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: December 15, 2003
Last modified: April 16, 2014
This is version 100 of the entry and version 2 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names