DAPA1_ARATH
ID DAPA1_ARATH Reviewed; 365 AA.
AC Q9LZX6; O49355; Q8VZQ1; Q9SW58;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 21-NOV-2003, sequence version 2.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic;
DE Short=HTPA synthase 1;
DE EC=4.3.3.7;
DE Flags: Precursor;
GN Name=DHDPS1; Synonyms=DHDPS, DHPS1; OrderedLocusNames=At3g60880;
GN ORFNames=T4C21_290;
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 [MRNA] (ISOFORM 2).
RX PubMed=8049377; DOI=10.1007/bf00043882;
RA Vauterin M., Jacobs M.;
RT "Isolation of a poplar and an Arabidopsis thaliana dihydrodipicolinate
RT synthase cDNA clone.";
RL Plant Mol. Biol. 25:545-550(1994).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [6]
RP NUCLEOTIDE SEQUENCE OF 1-159 (ISOFORM 2).
RA Vauterin M.;
RL Submitted (MAY-1996) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde
CC [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-
CC 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O; Xref=Rhea:RHEA:34171,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:67139, ChEBI:CHEBI:537519; EC=4.3.3.7;
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LZX6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LZX6-2; Sequence=VSP_009000;
CC -!- MISCELLANEOUS: [Isoform 1]: May be due to a competing acceptor splice
CC site.
CC -!- SIMILARITY: Belongs to the DapA family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a dihydrodipicolinate synthase
CC (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde
CC [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was
CC shown in E.coli that the product of the enzymatic reaction is not
CC dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-
CC dipicolinic acid (HTPA), and that the consecutive dehydration reaction
CC leading to DHDP is not spontaneous but catalyzed by DapB.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X72971; CAB45642.1; -; mRNA.
DR EMBL; AL162295; CAB82692.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80120.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80121.1; -; Genomic_DNA.
DR EMBL; AY063943; AAL36299.1; -; mRNA.
DR EMBL; AY096442; AAM20082.1; -; mRNA.
DR EMBL; AY087718; AAM65255.1; -; mRNA.
DR EMBL; X98080; CAA66703.1; -; Genomic_DNA.
DR PIR; S46304; S46304.
DR PIR; T47899; T47899.
DR RefSeq; NP_191647.1; NM_115952.2. [Q9LZX6-2]
DR RefSeq; NP_850730.1; NM_180399.3. [Q9LZX6-1]
DR PDB; 6VVH; X-ray; 1.79 A; AAA/BBB/CCC/DDD=49-365.
DR PDB; 6VVI; X-ray; 2.15 A; AAA/BBB/CCC/DDD=49-365.
DR PDB; 7MDS; X-ray; 2.29 A; A/B=49-365.
DR PDBsum; 6VVH; -.
DR PDBsum; 6VVI; -.
DR PDBsum; 7MDS; -.
DR AlphaFoldDB; Q9LZX6; -.
DR SMR; Q9LZX6; -.
DR BioGRID; 10573; 2.
DR STRING; 3702.AT3G60880.2; -.
DR PaxDb; Q9LZX6; -.
DR PRIDE; Q9LZX6; -.
DR ProteomicsDB; 224706; -. [Q9LZX6-1]
DR EnsemblPlants; AT3G60880.1; AT3G60880.1; AT3G60880. [Q9LZX6-2]
DR EnsemblPlants; AT3G60880.2; AT3G60880.2; AT3G60880. [Q9LZX6-1]
DR GeneID; 825259; -.
DR Gramene; AT3G60880.1; AT3G60880.1; AT3G60880. [Q9LZX6-2]
DR Gramene; AT3G60880.2; AT3G60880.2; AT3G60880. [Q9LZX6-1]
DR KEGG; ath:AT3G60880; -.
DR Araport; AT3G60880; -.
DR TAIR; locus:2101921; AT3G60880.
DR eggNOG; ENOG502QQ8M; Eukaryota.
DR InParanoid; Q9LZX6; -.
DR OMA; MYLTDGK; -.
DR OrthoDB; 1238597at2759; -.
DR PhylomeDB; Q9LZX6; -.
DR BioCyc; ARA:AT3G60880-MON; -.
DR UniPathway; UPA00034; UER00017.
DR PRO; PR:Q9LZX6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LZX6; baseline and differential.
DR Genevisible; Q9LZX6; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0008840; F:4-hydroxy-tetrahydrodipicolinate synthase activity; IDA:TAIR.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR CDD; cd00950; DHDPS; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00418; DapA; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR005263; DapA.
DR InterPro; IPR002220; DapA-like.
DR InterPro; IPR020625; Schiff_base-form_aldolases_AS.
DR InterPro; IPR020624; Schiff_base-form_aldolases_CS.
DR PANTHER; PTHR12128; PTHR12128; 1.
DR Pfam; PF00701; DHDPS; 1.
DR PRINTS; PR00146; DHPICSNTHASE.
DR SMART; SM01130; DHDPS; 1.
DR TIGRFAMs; TIGR00674; dapA; 1.
DR PROSITE; PS00665; DHDPS_1; 1.
DR PROSITE; PS00666; DHDPS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; Alternative splicing;
KW Amino-acid biosynthesis; Chloroplast; Diaminopimelate biosynthesis; Lyase;
KW Lysine biosynthesis; Plastid; Reference proteome; Schiff base;
KW Transit peptide.
FT TRANSIT 1..39
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 40..365
FT /note="4-hydroxy-tetrahydrodipicolinate synthase 1,
FT chloroplastic"
FT /id="PRO_0000007197"
FT ACT_SITE 194
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 222
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000250"
FT BINDING 108
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000250"
FT BINDING 261
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000250"
FT SITE 107
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000250"
FT SITE 170
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000250"
FT VAR_SEQ 30
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:8049377, ECO:0000303|Ref.5"
FT /id="VSP_009000"
FT CONFLICT 286
FT /note="A -> E (in Ref. 1; CAB45642)"
FT /evidence="ECO:0000305"
FT HELIX 60..64
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 84..96
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:7MDS"
FT TURN 107..110
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 116..130
FT /evidence="ECO:0007829|PDB:7MDS"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 175..186
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 191..195
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 197..200
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 206..213
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 227..234
FT /evidence="ECO:0007829|PDB:7MDS"
FT TURN 235..237
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 240..243
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 245..254
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 269..277
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 282..295
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 297..299
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 302..310
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 316..319
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 327..340
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 342..344
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 345..349
FT /evidence="ECO:0007829|PDB:7MDS"
FT HELIX 356..358
FT /evidence="ECO:0007829|PDB:7MDS"
FT STRAND 360..363
FT /evidence="ECO:0007829|PDB:7MDS"
SQ SEQUENCE 365 AA; 40620 MW; F07BBAE68F004484 CRC64;
MSALKNYGLI SIDSALHFPR SNQLQSYKRR NAKWVSPIAA VVPNFHLPMR SLEDKNRTNT
DDIRSLRVIT AIKTPYLPDG RFDLQAYDDL VNTQIENGAE GVIVGGTTGE GQLMSWDEHI
MLIGHTVNCF GGRIKVIGNT GSNSTREAIH ATEQGFAMGM HGALHINPYY GKTSIEGMNA
HFQTVLHMGP TIIYNVPGRT CQDIPPQVIF KLSQNPNMAG VKECVGNNRV EEYTEKGIVV
WSGNDDQCHD SRWDHGATGV ISVTSNLVPG LMRKLMFEGR NSALNAKLLP LMDWLFQEPN
PIGVNTALAQ LGVARPVFRL PYVPLPLSKR IEFVKLVKEI GREHFVGDRD VQVLDDDDFI
LIGRY
