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Protein

Diaminopimelate epimerase, chloroplastic

Gene

DAPF

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.1 Publication

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.

Enzyme regulationi

Inhibited by aziridino-diaminopimelate (AziDAP).

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase, chloroplastic (DAPF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei88Substrate1
Binding sitei141Substrate1
Active sitei1501
Binding sitei239Substrate1
Binding sitei278Substrate1
Active sitei3051

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciARA:AT3G53580-MONOMER.
BRENDAi5.1.1.7. 399.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimerase, chloroplastic (EC:5.1.1.7)
Short name:
DAP epimerase
Gene namesi
Name:DAPF
Ordered Locus Names:At3g53580
ORF Names:F4P12.280
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G53580.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
  • cytosol Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 52ChloroplastSequence analysisCombined sourcesAdd BLAST52
ChainiPRO_000030717953 – 362Diaminopimelate epimerase, chloroplasticAdd BLAST310

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei53N-acetylalanineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ9LFG2.
PRIDEiQ9LFG2.

Expressioni

Gene expression databases

GenevisibleiQ9LFG2. AT.

Interactioni

Protein-protein interaction databases

BioGridi9843. 1 interactor.
STRINGi3702.AT3G53580.1.

Structurei

Secondary structure

1362
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi66 – 73Combined sources8
Beta strandi77 – 85Combined sources9
Beta strandi88 – 94Combined sources7
Helixi105 – 111Combined sources7
Turni114 – 116Combined sources3
Beta strandi121 – 128Combined sources8
Beta strandi134 – 141Combined sources8
Helixi151 – 164Combined sources14
Beta strandi175 – 177Combined sources3
Beta strandi180 – 186Combined sources7
Beta strandi192 – 195Combined sources4
Helixi203 – 205Combined sources3
Beta strandi220 – 225Combined sources6
Beta strandi228 – 247Combined sources20
Helixi255 – 257Combined sources3
Helixi260 – 268Combined sources9
Beta strandi278 – 286Combined sources9
Beta strandi289 – 296Combined sources8
Turni297 – 299Combined sources3
Helixi306 – 318Combined sources13
Beta strandi324 – 330Combined sources7
Beta strandi333 – 339Combined sources7
Turni341 – 343Combined sources3
Beta strandi346 – 350Combined sources5
Beta strandi353 – 361Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EJXX-ray1.95A/B/C/D/E/F52-362[»]
3EKMX-ray2.30A/B/C/D/E/F52-362[»]
ProteinModelPortaliQ9LFG2.
SMRiQ9LFG2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9LFG2.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni151 – 152Substrate binding2
Regioni296 – 297Substrate binding2
Regioni306 – 307Substrate binding2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IHJB. Eukaryota.
COG0253. LUCA.
HOGENOMiHOG000220466.
InParanoidiQ9LFG2.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiEOG09360FF0.
PhylomeDBiQ9LFG2.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9LFG2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEIAAVSTVS VAPQSRRVSN AFSRNLGSVS SLSFGFFEKE YCFKSPSLRV
60 70 80 90 100
SAAASMDAVT AEKFSPASFL DKKETGVLHF VKYHGLGNDF ILVDNRDSSE
110 120 130 140 150
PKITQEQAAK LCDRNFGVGA DGVIFAMPGV NGTDYAMRIF NSDGSEPEMC
160 170 180 190 200
GNGVRCFARF IAELENLQGK HSFTIHTGAG LIVPEIQDDG QVKVDMGTPI
210 220 230 240 250
LKAQDVPTKL SGNKGEAVVE AELVVDGVSW NVTCVSMGNP HCITFGKKGG
260 270 280 290 300
PNLKVDDLNL PEIGPKFEHH EMFPARTNTE FVEVLSRSHL KMRVWERGAG
310 320 330 340 350
ATLACGTGAC ALVVAAVLEG RADRKCTVDL PGGPLEIEWK QEDNHIYMTG
360
PAEAVFYGSA LL
Length:362
Mass (Da):38,984
Last modified:October 1, 2000 - v1
Checksum:iB2C18C4714BAA543
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL132966 Genomic DNA. Translation: CAB67665.1.
CP002686 Genomic DNA. Translation: AEE79113.1.
AY126996 mRNA. Translation: AAM83223.1.
AY143871 mRNA. Translation: AAN28810.1.
PIRiT45898.
RefSeqiNP_190926.1. NM_115218.4.
UniGeneiAt.21032.

Genome annotation databases

EnsemblPlantsiAT3G53580.1; AT3G53580.1; AT3G53580.
GeneIDi824526.
GrameneiAT3G53580.1; AT3G53580.1; AT3G53580.
KEGGiath:AT3G53580.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL132966 Genomic DNA. Translation: CAB67665.1.
CP002686 Genomic DNA. Translation: AEE79113.1.
AY126996 mRNA. Translation: AAM83223.1.
AY143871 mRNA. Translation: AAN28810.1.
PIRiT45898.
RefSeqiNP_190926.1. NM_115218.4.
UniGeneiAt.21032.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EJXX-ray1.95A/B/C/D/E/F52-362[»]
3EKMX-ray2.30A/B/C/D/E/F52-362[»]
ProteinModelPortaliQ9LFG2.
SMRiQ9LFG2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi9843. 1 interactor.
STRINGi3702.AT3G53580.1.

Proteomic databases

PaxDbiQ9LFG2.
PRIDEiQ9LFG2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G53580.1; AT3G53580.1; AT3G53580.
GeneIDi824526.
GrameneiAT3G53580.1; AT3G53580.1; AT3G53580.
KEGGiath:AT3G53580.

Organism-specific databases

TAIRiAT3G53580.

Phylogenomic databases

eggNOGiENOG410IHJB. Eukaryota.
COG0253. LUCA.
HOGENOMiHOG000220466.
InParanoidiQ9LFG2.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiEOG09360FF0.
PhylomeDBiQ9LFG2.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciARA:AT3G53580-MONOMER.
BRENDAi5.1.1.7. 399.

Miscellaneous databases

EvolutionaryTraceiQ9LFG2.
PROiQ9LFG2.

Gene expression databases

GenevisibleiQ9LFG2. AT.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase. 1 hit.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDAPF_ARATH
AccessioniPrimary (citable) accession number: Q9LFG2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 23, 2007
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

This enzyme requires no cofactors.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.