Q9LFG2 (DAPF_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	362 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.
Enzyme regulation	Inhibited by aziridino-diaminopimelate (AziDAP).
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1.
Subcellular location	Plastid › chloroplast Potential.
Miscellaneous	This enzyme requires no cofactors.
Sequence similarities	Belongs to the diaminopimelate epimerase family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Lysine biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: InterPro
Cellular component	chloroplast stroma Inferred from direct assay. Source: TAIR
Molecular function	diaminopimelate epimerase activity Inferred from genetic interaction Ref.4. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 51

51

Chloroplast Potential

Chain

52 – 362

311

Diaminopimelate epimerase, chloroplastic

PRO_0000307179

Regions

Region

151 – 152

2

Substrate binding

Region

296 – 297

2

Substrate binding

Region

306 – 307

2

Substrate binding

Sites

Active site

150

1

Active site

305

1

Binding site

88

1

Substrate

Binding site

141

1

Substrate

Binding site

239

1

Substrate

Binding site

278

1

Substrate

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

362

Helix Strand Turn

Details...

Beta strand

81 – 84

4

Beta strand

90 – 94

5

Helix

105 – 111

7

Beta strand

124 – 127

4

Beta strand

135 – 139

5

Helix

155 – 164

10

Beta strand

182 – 186

5

Beta strand

192 – 195

4

Helix

203 – 205

3

Beta strand

220 – 224

5

Beta strand

229 – 236

8

Beta strand

240 – 244

5

Helix

255 – 257

3

Turn

260 – 262

3

Turn

266 – 269

4

Beta strand

278 – 286

9

Beta strand

289 – 295

7

Helix

310 – 318

9

Beta strand

324 – 329

6

Beta strand

335 – 339

5

Turn

341 – 343

3

Beta strand

346 – 349

4

Beta strand

353 – 356

4

Sequences

	Sequence		Length	Mass (Da)
	Q9LFG2 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: B2C18C4714BAA543	FASTA	362	38,984
	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

References

	« Hide 'large scale' referencesShow '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. , 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: 11130713] [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: 14593172] [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: 15652176] [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: 19013471] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 52-362 IN COMPLEX WITH INHIBITORS.
+	Additional computationally mapped references.

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.

IPI

IPI00545144.

PIR

T45898.

RefSeq

NP_190926.1. NM_115218.3.

UniGene

At.21032.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q9LFG2.

SMR

Q9LFG2. Positions 62-362.

ModBase

Search...

Protein-protein interaction databases

STRING

Q9LFG2.

Proteomic databases

PRIDE

Q9LFG2.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G53580.1; AT3G53580.1; AT3G53580.

GeneID

824526.

GenomeReviews

Gene locus AT3G53580 in contig BA000014_GR.

KEGG

ath:AT3G53580.

NMPDR

fig|3702.1.peg.16648.

Organism-specific databases

TAIR

At3g53580.

Phylogenomic databases

eggNOG

euNOG16969.

GeneTree

EPGT00050000005507.

HOGENOM

HBG399442.

InParanoid

Q9LFG2.

OMA

FMTGPAT.

PhylomeDB

Q9LFG2.

ProtClustDB

PLN02536.

Gene expression databases

Genevestigator

Q9LFG2.

Family and domain databases

InterPro

IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]

KO

K01778.

Pfam

PF01678. DAP_epimerase. 2 hits.
[Graphical view]

TIGRFAMs

TIGR00652. DapF. 1 hit.

PROSITE

PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DAPF_ARATH

Accession

Primary (citable) accession number: Q9LFG2

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 23, 2007
Last sequence update:	October 1, 2000
Last modified:	January 25, 2012
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program