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Protein

Peptide deformylase 1B, chloroplastic/mitochondrial

Gene

PDF1B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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.

Cofactori

Fe2+1 PublicationNote: 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-Ser1 Publication

Vmax=20 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide1 Publication

Vmax=1.3 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser1 Publication

Sites

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

GO - Molecular functioni

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

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.
BRENDAi3.5.1.88. 399.
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 Componenti: 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

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 mitochondrionSequence AnalysisAdd
BLAST
Chaini57 – 273217Peptide deformylase 1B, chloroplastic/mitochondrialPRO_0000006732Add
BLAST

Proteomic databases

PaxDbiQ9FUZ2.
PRIDEiQ9FUZ2.

Expressioni

Tissue specificityi

Expressed in leaves and flowers.1 Publication

Gene expression databases

GenevestigatoriQ9FUZ2.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi16595. 3 interactions.
IntActiQ9FUZ2. 2 interactions.

Structurei

Secondary structure

1
273
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi89 – 913Combined sources
Helixi103 – 11816Combined sources
Beta strandi122 – 1254Combined sources
Helixi126 – 1294Combined sources
Beta strandi133 – 1386Combined sources
Beta strandi150 – 16011Combined sources
Beta strandi164 – 1696Combined sources
Beta strandi179 – 1857Combined sources
Beta strandi187 – 1926Combined sources
Beta strandi194 – 1963Combined sources
Beta strandi198 – 2036Combined sources
Helixi205 – 21814Combined sources
Helixi223 – 2264Combined sources
Helixi229 – 2335Combined sources
Helixi236 – 25015Combined sources
Helixi258 – 2603Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9FUZ2.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiQ9FUZ2.
KOiK01462.
OMAiHEFDHLL.
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

        10         20         30         40         50
MAVCNCFLQA PPLSRILLPV LSRRATTLSA GYGRLKSTVT FCSTVNRTSP
60 70 80 90 100
LTSSVRAEVK RVSRKDDKVA SATDVQFETP LKIVEYPDPI LRAKNKRIDI
110 120 130 140 150
FDENLKNLVD AMFDVMYKTD GIGLSAPQVG LNVQLMVFNP AGEPGEGKEI
160 170 180 190 200
VLVNPKIKKY SDKLVPFDEG CLSFPGIYAE VVRPQSVKID ARDITGERFS
210 220 230 240 250
ISLSRLPARI FQHEYDHLEG VLFFDRMTDQ VLDSIREELE ALEKKYEEKT
260 270
GLPSPERVEA RQKRKAGVGF GKR
Length:273
Mass (Da):30,610
Last modified:December 15, 2003 - v2
Checksum:i25CDA90ED6D9603E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti48 – 481T → N in AAM62644 (Ref. 5) Curated
Sequence conflicti205 – 2051R → S in AAG33980 (PubMed:11060042).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi16595. 3 interactions.
IntActiQ9FUZ2. 2 interactions.

Proteomic databases

PaxDbiQ9FUZ2.
PRIDEiQ9FUZ2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT5G14660.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiQ9FUZ2.
KOiK01462.
OMAiHEFDHLL.
PhylomeDBiQ9FUZ2.

Enzyme and pathway databases

BioCyciARA:AT5G14660-MONOMER.
ARA:GQT-2354-MONOMER.
BRENDAi3.5.1.88. 399.
SABIO-RKQ9FUZ2.

Miscellaneous databases

EvolutionaryTraceiQ9FUZ2.

Gene expression databases

GenevestigatoriQ9FUZ2.

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.
ProtoNetiSearch...

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(1999) [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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-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(2002) [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 (FEB-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(2000) [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(2000) [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(2002) [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(2007) [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: April 1, 2015
This is version 106 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

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 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.