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Reviewed, UniProtKB/Swiss-Prot Q9FUZ2 (DEF1B_ARATH)

Last modified June 16, 2009. Version 63. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Peptide deformylase 1B, chloroplastic
      Short name=PDF 1B
      Short name=AtPDF1B
      Short name=AtDEF2
    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) [Complete proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

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Protein attributes

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

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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.

Cofactor

Binds 1 Fe2+ ion. Ref.6

Enzyme regulation

Inhibited by actinonin. Ref.6 Ref.5

Subunit structure

Homodimer. Ref.8

Subcellular location

Plastid › chloroplast stroma. Mitochondrion. Note: Reported by Ref.1 to be localized to chloroplast and mitochondria based on transient expression in an heterologous system. Ref.1 Ref.5

Tissue specificity

Expressed in leaves and flowers. Ref.1

Disruption phenotype

Albino. Ref.7

Sequence similarities

Belongs to the polypeptide deformylase family.

biophysicochemical properties

Kinetic parameters:

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

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

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Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentChloroplast
Mitochondrion
Plastid
   DomainTransit peptide
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete 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: UniProtKB-KW

peptide deformylase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 5656Chloroplast Potential
Chain57 – 273217Peptide deformylase 1B, chloroplastic
PRO_0000006732

Sites

Active site2141 By similarity
Metal binding1711Iron
Metal binding2131Iron
Metal binding2171Iron

Experimental info

Mutagenesis1781Y → A: Decrease in substrate affinity. Ref.8
Mutagenesis1781Y → F or R: Increase in substrate affinity. Ref.8
Sequence conflict481T → N in AAM62644. Ref.4
Sequence conflict2051R → S in AAG33980. Ref.1

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Sequences

Sequence LengthMass (Da)Tools
Q9FUZ2-1 [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

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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: 11060042] [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: 11130714] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[3]"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: 14593172] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[4]"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].
[5]"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: 11553738] [Abstract]
Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[6]"Distinctive features of the two classes of eukaryotic peptide deformylases."
Serero A., Giglione C., Meinnel T.
J. Mol. Biol. 314:695-708(2001) [PubMed: 11733990] [Abstract]
Cited for: COFACTOR, ENZYME REGULATION.
[7]"Control of protein life-span by N-terminal methionine excision."
Giglione C., Vallon O., Meinnel T.
EMBO J. 22:13-23(2003) [PubMed: 12505980] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
[8]"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: 18412546] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 65-257, HOMODIMERIZATION, MUTAGENESIS OF TYR-178.

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Cross-references

Sequence databases

AF269165 mRNA. Translation: AAG33980.1.
AL163792 Genomic DNA. Translation: CAB87633.1.
AY050879 mRNA. Translation: AAK92816.1.
AY096673 mRNA. Translation: AAM20307.1.
AY085417 mRNA. Translation: AAM62644.1.
IPIIPI00542984.
PIRT48639.
RefSeqNP_196970.1.
NP_850821.1.
UniGeneAt.5087

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
3CPMX-ray2.40A65-257[»]
ModBaseSearch...

Proteomic databases

PRIDEQ9FUZ2.

Genome annotation databases

GeneID831318.
GenomeReviewsGene locus AT5G14660 in contig BA000015_GR.
KEGGath:AT5G14660.
NMPDRfig|3702.1.peg.23602.

Organism-specific databases

TAIRAt5g14660.

Phylogenomic databases

OMAQ9FUZ2. YKTDGIG.

Enzyme and pathway databases

BRENDA3.5.1.88. 302.

Gene expression databases

ArrayExpressQ9FUZ2.
GermOnlineAT5G14660. Arabidopsis thaliana.

Family and domain databases

InterProIPR000181. Fmet_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
PANTHERPTHR10458. Fmet_deformylase. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
ProDomPD003844. Fmet_deformylase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

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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: June 16, 2009
This is version 63 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectPPAP (Plant Proteome Annotation Project)

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Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents