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Protein

Peptide deformylase 1A, chloroplastic/mitochondrial

Gene

PDF1A

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.1 Publication

Catalytic activityi

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

Cofactori

Zn2+1 PublicationNote: Binds 1 Zn2+ ion per subunit.1 Publication

Enzyme regulationi

Inhibited by actinonin.2 Publications

Kineticsi

  1. KM=240 µM for N-formyl-Met-Leu-rho-nitroanilide1 Publication
  2. KM=710 µM for N-formyl-Met-Ala-Ser1 Publication
  1. Vmax=0.11 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide1 Publication
  2. Vmax=0.20 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei187Substrate; via carbonyl oxygen1 Publication1
Metal bindingi188Zinc1
Metal bindingi230Zinc1
Active sitei2311
Metal bindingi234Zinc1

GO - Molecular functioni

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

GO - Biological processi

  • co-translational protein modification Source: TAIR
  • translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.5.1.88. 399.
SABIO-RKQ9FV53.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1A, chloroplastic/mitochondrial (EC:3.5.1.88)
Short name:
AtDEF1
Short name:
AtPDF1A
Short name:
PDF 1A
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:PDF1A
Synonyms:DEF1
Ordered Locus Names:At1g15390
ORF Names:F9L1.34, F9L1_34
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G15390.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast stroma Source: UniProtKB-SubCell
  • mitochondrion Source: TAIR
  • plant-type cell wall Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid

Pathology & Biotechi

Disruption phenotypei

No visible phenotype.1 Publication

Chemistry databases

ChEMBLiCHEMBL1075041.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 60Chloroplast and mitochondrionSequence analysisAdd BLAST60
ChainiPRO_000000673061 – 269Peptide deformylase 1A, chloroplastic/mitochondrialAdd BLAST209

Proteomic databases

PaxDbiQ9FV53.

Expressioni

Tissue specificityi

Expressed in roots, leaves, flowers and siliques.1 Publication

Gene expression databases

GenevisibleiQ9FV53. AT.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi23349. 1 interactor.
STRINGi3702.AT1G15390.1.

Chemistry databases

BindingDBiQ9FV53.

Structurei

Secondary structure

1269
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi89 – 91Combined sources3
Helixi100 – 102Combined sources3
Helixi106 – 121Combined sources16
Beta strandi125 – 128Combined sources4
Helixi129 – 132Combined sources4
Beta strandi138 – 143Combined sources6
Helixi145 – 148Combined sources4
Helixi153 – 159Combined sources7
Beta strandi164 – 179Combined sources16
Beta strandi181 – 188Combined sources8
Beta strandi191 – 209Combined sources19
Beta strandi215 – 221Combined sources7
Helixi222 – 235Combined sources14
Helixi240 – 242Combined sources3
Helixi252 – 254Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZXZX-ray2.80A/B79-267[»]
1ZY0X-ray2.90A/B79-267[»]
1ZY1X-ray3.00A/B79-267[»]
4JE6X-ray2.00A/B79-267[»]
4JE7X-ray2.10A/B79-267[»]
4JE8X-ray2.40A/B79-267[»]
ProteinModelPortaliQ9FV53.
SMRiQ9FV53.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9FV53.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni123 – 126Substrate binding4
Regioni191 – 196Dimerization6
Regioni236 – 254DimerizationAdd BLAST19

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
HOGENOMiHOG000243508.
InParanoidiQ9FV53.
KOiK01462.
OMAiCDDPVPT.
OrthoDBiEOG09360MKH.

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.

Q9FV53-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGLHRDEATA METLFRVSLR LLPVSAAVTC RSIRFPVSRP GSSHLLNRKL
60 70 80 90 100
YNLPTSSSSS LSTKAGWLLG LGEKKKKVDL PEIVASGDPV LHEKAREVDP
110 120 130 140 150
GEIGSERIQK IIDDMIKVMR LAPGVGLAAP QIGVPLRIIV LEDTKEYISY
160 170 180 190 200
APKEEILAQE RRHFDLMVMV NPVLKERSNK KALFFEGCLS VDGFRAAVER
210 220 230 240 250
YLEVVVTGYD RQGKRIEVNA SGWQARILQH ECDHLDGNLY VDKMVPRTFR
260
TVDNLDLPLA EGCPKLGPQ
Length:269
Mass (Da):29,996
Last modified:May 31, 2011 - v3
Checksum:iBDDF13CC38F319C3
GO

Sequence cautioni

The sequence AAD39667 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAK32873 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF250959 mRNA. Translation: AAG33973.1.
AC007591 Genomic DNA. Translation: AAD39667.1. Different initiation.
CP002684 Genomic DNA. Translation: AEE29315.1.
AF361861 mRNA. Translation: AAK32873.1. Different initiation.
AY129485 mRNA. Translation: AAM91071.1.
PIRiE86288.
RefSeqiNP_563974.1. NM_101408.3.
UniGeneiAt.11423.
At.19791.

Genome annotation databases

EnsemblPlantsiAT1G15390.1; AT1G15390.1; AT1G15390.
GeneIDi838109.
GrameneiAT1G15390.1; AT1G15390.1; AT1G15390.
KEGGiath:AT1G15390.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF250959 mRNA. Translation: AAG33973.1.
AC007591 Genomic DNA. Translation: AAD39667.1. Different initiation.
CP002684 Genomic DNA. Translation: AEE29315.1.
AF361861 mRNA. Translation: AAK32873.1. Different initiation.
AY129485 mRNA. Translation: AAM91071.1.
PIRiE86288.
RefSeqiNP_563974.1. NM_101408.3.
UniGeneiAt.11423.
At.19791.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZXZX-ray2.80A/B79-267[»]
1ZY0X-ray2.90A/B79-267[»]
1ZY1X-ray3.00A/B79-267[»]
4JE6X-ray2.00A/B79-267[»]
4JE7X-ray2.10A/B79-267[»]
4JE8X-ray2.40A/B79-267[»]
ProteinModelPortaliQ9FV53.
SMRiQ9FV53.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi23349. 1 interactor.
STRINGi3702.AT1G15390.1.

Chemistry databases

BindingDBiQ9FV53.
ChEMBLiCHEMBL1075041.

Proteomic databases

PaxDbiQ9FV53.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G15390.1; AT1G15390.1; AT1G15390.
GeneIDi838109.
GrameneiAT1G15390.1; AT1G15390.1; AT1G15390.
KEGGiath:AT1G15390.

Organism-specific databases

TAIRiAT1G15390.

Phylogenomic databases

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
HOGENOMiHOG000243508.
InParanoidiQ9FV53.
KOiK01462.
OMAiCDDPVPT.
OrthoDBiEOG09360MKH.

Enzyme and pathway databases

BRENDAi3.5.1.88. 399.
SABIO-RKQ9FV53.

Miscellaneous databases

EvolutionaryTraceiQ9FV53.
PROiQ9FV53.

Gene expression databases

GenevisibleiQ9FV53. 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 nameiDEF1A_ARATH
AccessioniPrimary (citable) accession number: Q9FV53
Secondary accession number(s): Q9XI30
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: May 31, 2011
Last modified: November 30, 2016
This is version 124 of the entry and version 3 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.