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Q9LFG2 (DAPF_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 80. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Diaminopimelate epimerase, chloroplastic

Short name=DAP epimerase
EC=5.1.1.7
Gene names
Name:DAPF
Ordered Locus Names:At3g53580
ORF Names:F4P12.280
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length362 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4

Catalytic activity

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate. HAMAP-Rule MF_00197

Enzyme regulation

Inhibited by aziridino-diaminopimelate (AziDAP). HAMAP-Rule MF_00197

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_00197

Subcellular location

Plastidchloroplast Potential HAMAP-Rule MF_00197.

Miscellaneous

This enzyme requires no cofactors.

Sequence similarities

Belongs to the diaminopimelate epimerase family.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 5151Chloroplast Potential
Chain52 – 362311Diaminopimelate epimerase, chloroplastic HAMAP-Rule MF_00197
PRO_0000307179

Regions

Region151 – 1522Substrate binding HAMAP-Rule MF_00197
Region296 – 2972Substrate binding HAMAP-Rule MF_00197
Region306 – 3072Substrate binding HAMAP-Rule MF_00197

Sites

Active site1501
Active site3051
Binding site881Substrate
Binding site1411Substrate
Binding site2391Substrate
Binding site2781Substrate

Secondary structure

................................................ 362
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9LFG2 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: B2C18C4714BAA543

FASTA36238,984
        10         20         30         40         50         60 
MEIAAVSTVS VAPQSRRVSN AFSRNLGSVS SLSFGFFEKE YCFKSPSLRV SAAASMDAVT 

        70         80         90        100        110        120 
AEKFSPASFL DKKETGVLHF VKYHGLGNDF ILVDNRDSSE PKITQEQAAK LCDRNFGVGA 

       130        140        150        160        170        180 
DGVIFAMPGV NGTDYAMRIF NSDGSEPEMC GNGVRCFARF IAELENLQGK HSFTIHTGAG 

       190        200        210        220        230        240 
LIVPEIQDDG QVKVDMGTPI LKAQDVPTKL SGNKGEAVVE AELVVDGVSW NVTCVSMGNP 

       250        260        270        280        290        300 
HCITFGKKGG PNLKVDDLNL PEIGPKFEHH EMFPARTNTE FVEVLSRSHL KMRVWERGAG 

       310        320        330        340        350        360 
ATLACGTGAC ALVVAAVLEG RADRKCTVDL PGGPLEIEWK QEDNHIYMTG PAEAVFYGSA 


LL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AL132966 Genomic DNA. Translation: CAB67665.1.
CP002686 Genomic DNA. Translation: AEE79113.1.
AY126996 mRNA. Translation: AAM83223.1.
AY143871 mRNA. Translation: AAN28810.1.
PIRT45898.
RefSeqNP_190926.1. NM_115218.3.
UniGeneAt.21032.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3EJXX-ray1.95A/B/C/D/E/F52-362[»]
3EKMX-ray2.30A/B/C/D/E/F52-362[»]
ProteinModelPortalQ9LFG2.
SMRQ9LFG2. Positions 62-362.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid9843. 1 interaction.
STRING3702.AT3G53580.1-P.

Proteomic databases

PaxDbQ9LFG2.
PRIDEQ9LFG2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G53580.1; AT3G53580.1; AT3G53580.
GeneID824526.
KEGGath:AT3G53580.

Organism-specific databases

TAIRAT3G53580.

Phylogenomic databases

eggNOGCOG0253.
HOGENOMHOG000220466.
InParanoidQ9LFG2.
KOK01778.
OMACFARFVL.
PhylomeDBQ9LFG2.
ProtClustDBPLN02536.

Enzyme and pathway databases

BioCycARA:AT3G53580-MONOMER.
UniPathwayUPA00034; UER00025.

Gene expression databases

GenevestigatorQ9LFG2.

Family and domain databases

HAMAPMF_00197. DAP_epimerase.
InterProIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERPTHR31689:SF0. PTHR31689:SF0. 1 hit.
PfamPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsTIGR00652. DapF. 1 hit.
PROSITEPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9LFG2.
PROQ9LFG2.

Entry information

Entry nameDAPF_ARATH
AccessionPrimary (citable) accession number: Q9LFG2
Entry history
Integrated into UniProtKB/Swiss-Prot: October 23, 2007
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names