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Protein

Peptide deformylase 1B, chloroplastic/mitochondrial

Gene

PDF1B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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
  1. Vmax=20 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide1 Publication
  2. Vmax=1.3 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi171Iron1
Metal bindingi213Iron1
Active sitei214By similarity1
Metal bindingi217Iron1

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • peptide deformylase activity Source: TAIR

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding

Enzyme and pathway databases

BRENDAi3.5.1.88 399
SABIO-RKiQ9FUZ2

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
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

AraportiAT5G14660
TAIRilocus:2222667 AT5G14660

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid

Pathology & Biotechi

Disruption phenotypei

Albino.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi178Y → A: Decrease in substrate affinity. 1 Publication1
Mutagenesisi178Y → F or R: Increase in substrate affinity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 56Chloroplast and mitochondrionSequence analysisAdd BLAST56
ChainiPRO_000000673257 – 273Peptide deformylase 1B, chloroplastic/mitochondrialAdd BLAST217

Proteomic databases

PaxDbiQ9FUZ2
PRIDEiQ9FUZ2

PTM databases

iPTMnetiQ9FUZ2

Expressioni

Tissue specificityi

Expressed in leaves and flowers.1 Publication

Gene expression databases

ExpressionAtlasiQ9FUZ2 differential
GenevisibleiQ9FUZ2 AT

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi16595, 3 interactors
IntActiQ9FUZ2, 2 interactors
STRINGi3702.AT5G14660.1

Structurei

Secondary structure

1273
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi89 – 91Combined sources3
Helixi103 – 118Combined sources16
Beta strandi122 – 125Combined sources4
Helixi126 – 129Combined sources4
Beta strandi133 – 138Combined sources6
Beta strandi150 – 160Combined sources11
Beta strandi164 – 169Combined sources6
Beta strandi179 – 185Combined sources7
Beta strandi187 – 192Combined sources6
Beta strandi194 – 196Combined sources3
Beta strandi198 – 203Combined sources6
Helixi205 – 218Combined sources14
Helixi223 – 226Combined sources4
Helixi229 – 233Combined sources5
Helixi236 – 250Combined sources15
Helixi258 – 260Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9FUZ2

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG3137 Eukaryota
COG0242 LUCA
HOGENOMiHOG000243509
InParanoidiQ9FUZ2
KOiK01462
OMAiHEFDHLL
OrthoDBiEOG09360NFS
PhylomeDBiQ9FUZ2

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
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)DescriptionActionsGraphical viewLength
Sequence conflicti48T → N in AAM62644 (Ref. 5) Curated1
Sequence conflicti205R → S in AAG33980 (PubMed:11060042).Curated1

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
CP002688 Genomic DNA Translation: ANM71170.1
AY050879 mRNA Translation: AAK92816.1
AY096673 mRNA Translation: AAM20307.1
AY085417 mRNA Translation: AAM62644.1
PIRiT48639
RefSeqiNP_001332718.1, NM_001343352.1
NP_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
AT5G14660.3; AT5G14660.3; AT5G14660
GeneIDi831318
GrameneiAT5G14660.1; AT5G14660.1; AT5G14660
AT5G14660.2; AT5G14660.2; AT5G14660
AT5G14660.3; AT5G14660.3; AT5G14660
KEGGiath:AT5G14660

Similar proteinsi

Entry informationi

Entry nameiDEF1B_ARATH
AccessioniPrimary (citable) accession number: Q9FUZ2
Secondary accession number(s): Q8LEH0, Q949U8, Q9LYJ4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: December 15, 2003
Last modified: May 23, 2018
This is version 124 of the entry and version 2 of the sequence. See 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
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Main funding by: National Institutes of Health