DAPB2_ARATH
ID DAPB2_ARATH Reviewed; 349 AA.
AC Q8LB01; Q3EAH1; Q9M1Y5;
DT 23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic;
DE Short=HTPA reductase 2;
DE EC=1.17.1.8;
DE Flags: Precursor;
GN Name=DAPB2; OrderedLocusNames=At3g59890; ORFNames=F24G16.160;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION.
RX PubMed=15652176; DOI=10.1016/j.bbagen.2004.09.008;
RA Hudson A.O., Bless C., Macedo P., Chatterjee S.P., Singh B.K., Gilvarg C.,
RA Leustek T.;
RT "Biosynthesis of lysine in plants: evidence for a variant of the known
RT bacterial pathways.";
RL Biochim. Biophys. Acta 1721:27-36(2005).
CC -!- FUNCTION: Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate
CC (HTPA) to tetrahydrodipicolinate. {ECO:0000305|PubMed:15652176}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-
CC hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH;
CC Xref=Rhea:RHEA:35323, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16845, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:67139; EC=1.17.1.8;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-
CC 4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH;
CC Xref=Rhea:RHEA:35331, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16845, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:67139; EC=1.17.1.8;
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8LB01-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8LB01-2; Sequence=VSP_028629;
CC -!- SIMILARITY: Belongs to the DapB family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a dihydrodipicolinate reductase
CC (DHDPR), catalyzing the conversion of dihydrodipicolinate to
CC tetrahydrodipicolinate. However, it was shown in E.coli that the
CC substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP)
CC but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid
CC (HTPA), the product released by the DapA-catalyzed reaction.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB75808.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL138647; CAB75808.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE79981.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79982.1; -; Genomic_DNA.
DR EMBL; AY087505; AAM65048.1; -; mRNA.
DR EMBL; BT026511; ABH04618.1; -; mRNA.
DR PIR; T47813; T47813.
DR RefSeq; NP_567088.1; NM_115852.4. [Q8LB01-1]
DR RefSeq; NP_974464.1; NM_202735.1. [Q8LB01-2]
DR PDB; 5UA0; X-ray; 2.30 A; A/B/C=54-349.
DR PDBsum; 5UA0; -.
DR AlphaFoldDB; Q8LB01; -.
DR SMR; Q8LB01; -.
DR STRING; 3702.AT3G59890.1; -.
DR iPTMnet; Q8LB01; -.
DR PaxDb; Q8LB01; -.
DR PRIDE; Q8LB01; -.
DR ProteomicsDB; 224707; -. [Q8LB01-1]
DR EnsemblPlants; AT3G59890.1; AT3G59890.1; AT3G59890. [Q8LB01-1]
DR EnsemblPlants; AT3G59890.2; AT3G59890.2; AT3G59890. [Q8LB01-2]
DR GeneID; 825159; -.
DR Gramene; AT3G59890.1; AT3G59890.1; AT3G59890. [Q8LB01-1]
DR Gramene; AT3G59890.2; AT3G59890.2; AT3G59890. [Q8LB01-2]
DR KEGG; ath:AT3G59890; -.
DR Araport; AT3G59890; -.
DR TAIR; locus:2080482; AT3G59890.
DR eggNOG; ENOG502QPSY; Eukaryota.
DR InParanoid; Q8LB01; -.
DR OMA; PINHEYM; -.
DR PhylomeDB; Q8LB01; -.
DR BioCyc; ARA:AT3G59890-MON; -.
DR BRENDA; 1.17.1.8; 399.
DR UniPathway; UPA00034; UER00018.
DR PRO; PR:Q8LB01; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8LB01; baseline and differential.
DR Genevisible; Q8LB01; AT.
DR GO; GO:0009570; C:chloroplast stroma; IBA:GO_Central.
DR GO; GO:0008839; F:4-hydroxy-tetrahydrodipicolinate reductase; IBA:GO_Central.
DR GO; GO:0070402; F:NADPH binding; IEA:InterPro.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR InterPro; IPR022663; DapB_C.
DR InterPro; IPR000846; DapB_N.
DR InterPro; IPR023940; DHDPR_bac.
DR InterPro; IPR011859; Dihydrodipicolinate_Rdtase_pln.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR20836; PTHR20836; 1.
DR Pfam; PF05173; DapB_C; 1.
DR Pfam; PF01113; DapB_N; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR02130; dapB_plant; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Amino-acid biosynthesis; Chloroplast;
KW Diaminopimelate biosynthesis; Lysine biosynthesis; NAD; NADP;
KW Oxidoreductase; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..53
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 54..349
FT /note="4-hydroxy-tetrahydrodipicolinate reductase 2,
FT chloroplastic"
FT /id="PRO_0000307183"
FT ACT_SITE 232
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 236
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 81..86
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 173..175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 196..199
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 241..242
FT /ligand="(S)-2,3,4,5-tetrahydrodipicolinate"
FT /ligand_id="ChEBI:CHEBI:16845"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..6
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_028629"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:5UA0"
FT TURN 81..83
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 85..96
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:5UA0"
FT TURN 109..113
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 131..141
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 156..166
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 170..172
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 179..189
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 201..216
FT /evidence="ECO:0007829|PDB:5UA0"
FT TURN 218..223
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 225..231
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 232..236
FT /evidence="ECO:0007829|PDB:5UA0"
FT TURN 237..239
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 240..252
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 263..265
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 267..282
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 285..293
FT /evidence="ECO:0007829|PDB:5UA0"
FT STRAND 300..307
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 311..329
FT /evidence="ECO:0007829|PDB:5UA0"
FT HELIX 339..345
FT /evidence="ECO:0007829|PDB:5UA0"
SQ SEQUENCE 349 AA; 37870 MW; D7CA92482ECA28CA CRC64;
MAANGLMAAS SVFLHRPVHP HFSFSSRTNQ MVPLGFKGRV SFIGNVKRCF PVVLSMGKSE
TFEEAGNSVA PGNGISIMVN GCSGKMGKAV IKAADSAGVN IVPTSFGSVE EAGQTVEVCG
KEILVHGPTE REKVLSSVFE KYPELIVVDY TIPSAVNDNA ELYGKVGVPF VMGTTGGDRT
RLYKTVEESK IYAVISPQMG KQVVAFLAAM EIMSEQFPGA FAGYSLEVME SHQASKLDAS
GTAKAVISCF QKLGVSYDMD QIQLIRDPKQ QIEVVGVPEE HVSGHAFHLY HLTSPDKTVS
FEFQHNVCGR SIYAEGTVDA VLFLAKKIRS KAEKRIYNMI DVLREGNMR
