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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
  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

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

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
Proteomesi
  • UP000006548 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

  • chloroplast Source: TAIR
  • chloroplast stroma Source: UniProtKB-SubCell
  • mitochondrion Source: UniProtKB-SubCell
Complete GO annotation...

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.

PTM databases

iPTMnetiQ9FUZ2.

Expressioni

Tissue specificityi

Expressed in leaves and flowers.1 Publication

Gene expression databases

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.
OMAiAVCNCFL.
OrthoDBiEOG09360NFS.
PhylomeDBiQ9FUZ2.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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)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.
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.
GrameneiAT5G14660.1; AT5G14660.1; AT5G14660.
AT5G14660.2; AT5G14660.2; AT5G14660.
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
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...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ9FUZ2.

Proteomic databases

PaxDbiQ9FUZ2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G14660.1; AT5G14660.1; AT5G14660.
AT5G14660.2; AT5G14660.2; AT5G14660.
GeneIDi831318.
GrameneiAT5G14660.1; AT5G14660.1; AT5G14660.
AT5G14660.2; AT5G14660.2; AT5G14660.
KEGGiath:AT5G14660.

Organism-specific databases

TAIRiAT5G14660.

Phylogenomic databases

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
HOGENOMiHOG000243509.
InParanoidiQ9FUZ2.
KOiK01462.
OMAiAVCNCFL.
OrthoDBiEOG09360NFS.
PhylomeDBiQ9FUZ2.

Enzyme and pathway databases

BRENDAi3.5.1.88. 399.
SABIO-RKQ9FUZ2.

Miscellaneous databases

EvolutionaryTraceiQ9FUZ2.
PROiQ9FUZ2.

Gene expression databases

GenevisibleiQ9FUZ2. AT.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

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: November 2, 2016
This is version 115 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

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 one 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.