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Q9LFG2

- DAPF_ARATH

UniProt

Q9LFG2 - DAPF_ARATH

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Protein

Diaminopimelate epimerase, chloroplastic

Gene

DAPF

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei88 – 881Substrate
Binding sitei141 – 1411Substrate
Active sitei150 – 1501
Binding sitei239 – 2391Substrate
Binding sitei278 – 2781Substrate
Active sitei305 – 3051

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: TAIR

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciARA:AT3G53580-MONOMER.
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
ProteomesiUP000006548: Chromosome 3

Organism-specific databases

TAIRiAT3G53580.

Subcellular locationi

Plastidchloroplast Curated

GO - Cellular componenti

  1. chloroplast Source: TAIR
  2. chloroplast stroma Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 5151ChloroplastSequence AnalysisAdd
BLAST
Chaini52 – 362311Diaminopimelate epimerase, chloroplasticPRO_0000307179Add
BLAST

Proteomic databases

PaxDbiQ9LFG2.
PRIDEiQ9LFG2.

Expressioni

Gene expression databases

GenevestigatoriQ9LFG2.

Interactioni

Protein-protein interaction databases

BioGridi9843. 1 interaction.
STRINGi3702.AT3G53580.1-P.

Structurei

Secondary structure

1
362
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi77 – 859Combined sources
Beta strandi88 – 947Combined sources
Helixi105 – 1117Combined sources
Turni114 – 1163Combined sources
Beta strandi121 – 1288Combined sources
Beta strandi134 – 1418Combined sources
Helixi151 – 16414Combined sources
Beta strandi175 – 1773Combined sources
Beta strandi180 – 1867Combined sources
Beta strandi192 – 1954Combined sources
Helixi203 – 2053Combined sources
Beta strandi220 – 2256Combined sources
Beta strandi228 – 24720Combined sources
Helixi255 – 2573Combined sources
Helixi260 – 2689Combined sources
Beta strandi278 – 2869Combined sources
Beta strandi289 – 2968Combined sources
Turni297 – 2993Combined sources
Helixi306 – 31813Combined sources
Beta strandi324 – 3307Combined sources
Beta strandi333 – 3397Combined sources
Turni341 – 3433Combined sources
Beta strandi346 – 3505Combined sources
Beta strandi353 – 3619Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EJXX-ray1.95A/B/C/D/E/F52-362[»]
3EKMX-ray2.30A/B/C/D/E/F52-362[»]
ProteinModelPortaliQ9LFG2.
SMRiQ9LFG2. Positions 62-362.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9LFG2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni151 – 1522Substrate binding
Regioni296 – 2972Substrate binding
Regioni306 – 3072Substrate binding

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
InParanoidiQ9LFG2.
KOiK01778.
OMAiLIVEPPY.
PhylomeDBiQ9LFG2.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
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_115218.3.
UniGeneiAt.21032.

Genome annotation databases

EnsemblPlantsiAT3G53580.1; AT3G53580.1; AT3G53580.
GeneIDi824526.
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 .
PIRi T45898.
RefSeqi NP_190926.1. NM_115218.3.
UniGenei At.21032.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3EJX X-ray 1.95 A/B/C/D/E/F 52-362 [» ]
3EKM X-ray 2.30 A/B/C/D/E/F 52-362 [» ]
ProteinModelPortali Q9LFG2.
SMRi Q9LFG2. Positions 62-362.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 9843. 1 interaction.
STRINGi 3702.AT3G53580.1-P.

Proteomic databases

PaxDbi Q9LFG2.
PRIDEi Q9LFG2.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT3G53580.1 ; AT3G53580.1 ; AT3G53580 .
GeneIDi 824526.
KEGGi ath:AT3G53580.

Organism-specific databases

TAIRi AT3G53580.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
InParanoidi Q9LFG2.
KOi K01778.
OMAi LIVEPPY.
PhylomeDBi Q9LFG2.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci ARA:AT3G53580-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q9LFG2.
PROi Q9LFG2.

Gene expression databases

Genevestigatori Q9LFG2.

Family and domain databases

HAMAPi MF_00197. DAP_epimerase.
InterProi IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view ]
PANTHERi PTHR31689. PTHR31689. 1 hit.
Pfami PF01678. DAP_epimerase. 2 hits.
[Graphical view ]
TIGRFAMsi TIGR00652. DapF. 1 hit.
PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways."
    Hudson A.O., Bless C., Macedo P., Chatterjee S.P., Singh B.K., Gilvarg C., Leustek T.
    Biochim. Biophys. Acta 1721:27-36(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis."
    Pillai B., Moorthie V.A., van Belkum M.J., Marcus S.L., Cherney M.M., Diaper C.M., Vederas J.C., James M.N.
    J. Mol. Biol. 385:580-594(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 52-362 IN COMPLEX WITH INHIBITORS.

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 26, 2014
This is version 84 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

External Data

Dasty 3