DAPA_METJA
ID DAPA_METJA Reviewed; 289 AA.
AC Q57695;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=4-hydroxy-tetrahydrodipicolinate synthase {ECO:0000255|HAMAP-Rule:MF_00418};
DE Short=HTPA synthase {ECO:0000255|HAMAP-Rule:MF_00418};
DE EC=4.3.3.7 {ECO:0000255|HAMAP-Rule:MF_00418};
GN Name=dapA {ECO:0000255|HAMAP-Rule:MF_00418}; OrderedLocusNames=MJ0244;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND SUBUNIT.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=20054116; DOI=10.1107/s174430910904651x;
RA Padmanabhan B., Strange R.W., Antonyuk S.V., Ellis M.J., Hasnain S.S.,
RA Iino H., Agari Y., Bessho Y., Yokoyama S.;
RT "Structure of dihydrodipicolinate synthase from Methanocaldococcus
RT jannaschii.";
RL Acta Crystallogr. F 65:1222-1226(2009).
CC -!- FUNCTION: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde
CC [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
CC {ECO:0000255|HAMAP-Rule:MF_00418}.
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 Evidence={ECO:0000255|HAMAP-Rule:MF_00418};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4.
CC {ECO:0000255|HAMAP-Rule:MF_00418}.
CC -!- SUBUNIT: Homotetramer; dimer of dimers. {ECO:0000255|HAMAP-
CC Rule:MF_00418, ECO:0000269|PubMed:20054116}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00418}.
CC -!- SIMILARITY: Belongs to the DapA family. {ECO:0000255|HAMAP-
CC Rule:MF_00418}.
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}.
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DR EMBL; L77117; AAB98232.1; -; Genomic_DNA.
DR PIR; E64330; E64330.
DR RefSeq; WP_010869742.1; NC_000909.1.
DR PDB; 2YXG; X-ray; 2.20 A; A/B/C/D=1-289.
DR PDBsum; 2YXG; -.
DR AlphaFoldDB; Q57695; -.
DR SMR; Q57695; -.
DR STRING; 243232.MJ_0244; -.
DR EnsemblBacteria; AAB98232; AAB98232; MJ_0244.
DR GeneID; 1451098; -.
DR KEGG; mja:MJ_0244; -.
DR eggNOG; arCOG04172; Archaea.
DR HOGENOM; CLU_049343_7_0_2; -.
DR InParanoid; Q57695; -.
DR OMA; GMDACVP; -.
DR OrthoDB; 65776at2157; -.
DR PhylomeDB; Q57695; -.
DR BRENDA; 4.3.3.7; 3260.
DR UniPathway; UPA00034; UER00017.
DR EvolutionaryTrace; Q57695; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008675; F:2-dehydro-3-deoxy-phosphogluconate aldolase activity; IEA:UniProt.
DR GO; GO:0008840; F:4-hydroxy-tetrahydrodipicolinate synthase activity; IBA:GO_Central.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IEA:UniProtKB-UniRule.
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 PIRSF; PIRSF001365; 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; Amino-acid biosynthesis; Cytoplasm;
KW Diaminopimelate biosynthesis; Lyase; Lysine biosynthesis;
KW Reference proteome; Schiff base.
FT CHAIN 1..289
FT /note="4-hydroxy-tetrahydrodipicolinate synthase"
FT /id="PRO_0000103197"
FT ACT_SITE 132
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT ACT_SITE 161
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT BINDING 44
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT BINDING 201
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT SITE 43
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT SITE 106
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 20..32
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:2YXG"
FT TURN 43..46
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 52..66
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 69..75
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 81..94
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 111..124
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 144..153
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 168..176
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 179..184
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 186..188
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 189..194
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 199..203
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 209..221
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 224..240
FT /evidence="ECO:0007829|PDB:2YXG"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 248..256
FT /evidence="ECO:0007829|PDB:2YXG"
FT HELIX 273..285
FT /evidence="ECO:0007829|PDB:2YXG"
SQ SEQUENCE 289 AA; 31580 MW; 34CD8619C4A53CCA CRC64;
MFKGVYPAII TPFKNKEVDF DGLEENINFL IENGVSGIVA VGTTGESPTL SHEEHKKVIE
KVVDVVNGRV QVIAGAGSNC TEEAIELSVF AEDVGADAVL SITPYYNKPT QEGLRKHFGK
VAESINLPIV LYNVPSRTAV NLEPKTVKLL AEEYSNISAV KEANPNLSQV SELIHDAKIT
VLSGNDELTL PIIALGGKGV ISVVANIVPK EFVEMVNYAL EGDFEKAREI HYKLFPLMKA
MFIETNPIPV KTALNMMGRP AGELRLPLCE MSEEHKKILE NVLKDLGLI
