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Protein

Peptide deformylase 1A, chloroplastic/mitochondrial

Gene

PDF1A

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.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

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandMetal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.5.1.88 399
SABIO-RKiQ9FV53

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

AraportiAT1G15390
TAIRilocus:2037733 AT1G15390

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

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

ExpressionAtlasiQ9FV53 baseline and differential
GenevisibleiQ9FV53 AT

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi233491 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
OMAiVCQVGDP
OrthoDBiEOG09360MKH

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.101 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.

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

Similar proteinsi

Entry informationi

Entry nameiDEF1A_ARATH
AccessioniPrimary (citable) accession number: Q9FV53
Secondary accession number(s): Q9XI30
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: May 31, 2011
Last modified: April 25, 2018
This is version 131 of the entry and version 3 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