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Q9FUZ2

- DEF1B_ARATH

UniProt

Q9FUZ2 - DEF1B_ARATH

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Protein
Peptide deformylase 1B, chloroplastic/mitochondrial
Gene
PDF1B, DEF2, At5g14660, T15N1_150
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Binds 1 Fe2+ ion.1 Publication

Enzyme regulationi

Inhibited by actinonin.2 Publications

Kineticsi

  1. KM=130 µM for N-formyl-Met-Leu-rho-nitroanilide1 Publication
  2. 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi171 – 1711Iron
Metal bindingi213 – 2131Iron
Active sitei214 – 2141 By similarity
Metal bindingi217 – 2171Iron

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: TAIR
Complete GO annotation...

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

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

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1B, chloroplastic/mitochondrial (EC:3.5.1.88)
Short name:
AtDEF2
Short name:
AtPDF1B
Short name:
PDF 1B
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:PDF1B
Synonyms:DEF2
Ordered Locus Names:At5g14660
ORF Names:T15N1_150
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 5

Organism-specific databases

TAIRiAT5G14660.

Subcellular locationi

Plastidchloroplast stroma. Mitochondrion
Note: Reported to be localized to chloroplast and mitochondria based on transient GFP expression in a heterologous system (1 Publication).2 Publications

GO - Cellular componenti

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

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid

Pathology & Biotechi

Disruption phenotypei

Albino.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi178 – 1781Y → A: Decrease in substrate affinity. 1 Publication
Mutagenesisi178 – 1781Y → F or R: Increase in substrate affinity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 5656Chloroplast and mitochondrion Reviewed prediction
Add
BLAST
Chaini57 – 273217Peptide deformylase 1B, chloroplastic/mitochondrialUniRule annotation
PRO_0000006732Add
BLAST

Proteomic databases

PaxDbiQ9FUZ2.
PRIDEiQ9FUZ2.

Expressioni

Tissue specificityi

Expressed in leaves and flowers.1 Publication

Gene expression databases

GenevestigatoriQ9FUZ2.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi16595. 3 interactions.
IntActiQ9FUZ2. 2 interactions.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi89 – 913
Helixi103 – 11816
Beta strandi122 – 1254
Helixi126 – 1294
Beta strandi133 – 1386
Beta strandi150 – 16011
Beta strandi164 – 1696
Beta strandi179 – 1857
Beta strandi187 – 1926
Beta strandi194 – 1963
Beta strandi198 – 2036
Helixi205 – 21814
Helixi223 – 2264
Helixi229 – 2335
Helixi236 – 25015
Helixi258 – 2603

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliQ9FUZ2.
SMRiQ9FUZ2. Positions 74-257.

Miscellaneous databases

EvolutionaryTraceiQ9FUZ2.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiQ9FUZ2.
KOiK01462.
OMAiTIMYKEG.
PhylomeDBiQ9FUZ2.

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.

Q9FUZ2-1 [UniParc]FASTAAdd to Basket

« Hide

MAVCNCFLQA PPLSRILLPV LSRRATTLSA GYGRLKSTVT FCSTVNRTSP    50
LTSSVRAEVK RVSRKDDKVA SATDVQFETP LKIVEYPDPI LRAKNKRIDI 100
FDENLKNLVD AMFDVMYKTD GIGLSAPQVG LNVQLMVFNP AGEPGEGKEI 150
VLVNPKIKKY SDKLVPFDEG CLSFPGIYAE VVRPQSVKID ARDITGERFS 200
ISLSRLPARI FQHEYDHLEG VLFFDRMTDQ VLDSIREELE ALEKKYEEKT 250
GLPSPERVEA RQKRKAGVGF GKR 273
Length:273
Mass (Da):30,610
Last modified:December 15, 2003 - v2
Checksum:i25CDA90ED6D9603E
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti48 – 481T → N in AAM62644. 1 Publication
Sequence conflicti205 – 2051R → S in AAG33980. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiT48639.
RefSeqiNP_196970.1. NM_121470.3.
NP_850821.1. NM_180490.1.
UniGeneiAt.5087.

Genome annotation databases

EnsemblPlantsiAT5G14660.1; AT5G14660.1; AT5G14660.
AT5G14660.2; AT5G14660.2; AT5G14660.
GeneIDi831318.
KEGGiath:AT5G14660.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi T48639.
RefSeqi NP_196970.1. NM_121470.3.
NP_850821.1. NM_180490.1.
UniGenei At.5087.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3CPM X-ray 2.40 A 65-257 [» ]
3M6O X-ray 2.00 A/B 83-273 [» ]
3M6P X-ray 2.00 A/B 83-273 [» ]
3M6Q X-ray 2.40 A 83-273 [» ]
3M6R X-ray 2.40 A/B/C/D 83-273 [» ]
3O3J X-ray 3.00 A 83-273 [» ]
3PN2 X-ray 2.00 A 83-273 [» ]
3PN3 X-ray 1.30 A/B 83-273 [» ]
3PN4 X-ray 1.90 A 83-273 [» ]
3PN5 X-ray 2.30 A 83-273 [» ]
3PN6 X-ray 2.10 A/B 83-273 [» ]
ProteinModelPortali Q9FUZ2.
SMRi Q9FUZ2. Positions 74-257.
ModBasei Search...

Protein-protein interaction databases

BioGridi 16595. 3 interactions.
IntActi Q9FUZ2. 2 interactions.

Proteomic databases

PaxDbi Q9FUZ2.
PRIDEi Q9FUZ2.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT5G14660.1 ; AT5G14660.1 ; AT5G14660 .
AT5G14660.2 ; AT5G14660.2 ; AT5G14660 .
GeneIDi 831318.
KEGGi ath:AT5G14660.

Organism-specific databases

TAIRi AT5G14660.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
InParanoidi Q9FUZ2.
KOi K01462.
OMAi TIMYKEG.
PhylomeDBi Q9FUZ2.

Enzyme and pathway databases

BioCyci ARA:AT5G14660-MONOMER.
ARA:GQT-2354-MONOMER.
SABIO-RK Q9FUZ2.

Miscellaneous databases

EvolutionaryTracei Q9FUZ2.

Gene expression databases

Genevestigatori Q9FUZ2.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.
    , 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.

Entry informationi

Entry nameiDEF1B_ARATH
AccessioniPrimary (citable) accession number: Q9FUZ2
Secondary accession number(s): Q8LEH0, Q949U8, Q9LYJ4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: December 15, 2003
Last modified: May 14, 2014
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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