DAPA_RHIML
ID DAPA_RHIML Reviewed; 292 AA.
AC Q07607;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2013, sequence version 2.
DT 03-AUG-2022, entry version 96.
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};
DE AltName: Full=Protein MosA;
GN Name=dapA {ECO:0000255|HAMAP-Rule:MF_00418}; Synonyms=mosA;
OS Rhizobium meliloti (Ensifer meliloti) (Sinorhizobium meliloti).
OG Plasmid pSym {ECO:0000303|PubMed:14672649}.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=382;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=L5-30; PLASMID=pSym;
RX PubMed=8349559; DOI=10.1128/jb.175.16.5193-5204.1993;
RA Murphy P.J., Trenz S.P., Grzemski W., de Bruijn F.J., Schell J.;
RT "The Rhizobium meliloti rhizopine mos locus is a mosaic structure
RT facilitating its symbiotic regulation.";
RL J. Bacteriol. 175:5193-5204(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES,
RP ACTIVITY REGULATION, IDENTIFICATION BY MASS SPECTROMETRY, AND
RP COMPLEMENTATION OF E.COLI DAPA MUTANT.
RC STRAIN=L5-30; PLASMID=pSym;
RX PubMed=14672649; DOI=10.1016/j.jmb.2003.10.063;
RA Tam P.H., Phenix C.P., Palmer D.R.;
RT "MosA, a protein implicated in rhizopine biosynthesis in Sinorhizobium
RT meliloti L5-30, is a dihydrodipicolinate synthase.";
RL J. Mol. Biol. 335:393-397(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 1-289 IN COMPLEX WITH PYRUVATE,
RP FUNCTION, ACTIVE SITES, ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=L5-30;
RX PubMed=18536061; DOI=10.1002/cbic.200700569;
RA Phenix C.P., Nienaber K., Tam P.H., Delbaere L.T., Palmer D.R.;
RT "Structural, functional and calorimetric investigation of MosA, a
RT dihydrodipicolinate synthase from Sinorhizobium meliloti l5-30, does not
RT support involvement in rhizopine biosynthesis.";
RL ChemBioChem 9:1591-1602(2008).
CC -!- FUNCTION: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde
CC [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
CC {ECO:0000305|PubMed:14672649, ECO:0000305|PubMed:18536061}.
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 -!- ACTIVITY REGULATION: Is feedback inhibited by lysine. Is competitively
CC inhibited by 2-oxobutyrate with respect to pyruvate.
CC {ECO:0000269|PubMed:14672649, ECO:0000269|PubMed:18536061}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.19 mM for pyruvate {ECO:0000269|PubMed:14672649};
CC KM=0.12 mM for L-aspartate-4-semialdehyde
CC {ECO:0000269|PubMed:14672649};
CC Note=kcat is 4.0 sec(-1).;
CC pH dependence:
CC Optimum pH is 7.7. {ECO:0000269|PubMed:14672649};
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. {ECO:0000269|PubMed:18536061}.
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 involved in the biosynthesis of a
CC rhizopine, catalyzing the conversion of scyllo-inosamine to 3-O-methyl-
CC scyllo-inosamine (PubMed:8349559). However, does not show
CC methyltransferase activity in the presence of scyllo-inosamine and S-
CC adenosylmethionine (SAM), and does not interact with rhizopines and SAM
CC (PubMed:18536061). {ECO:0000305|PubMed:18536061,
CC ECO:0000305|PubMed:8349559}.
CC -!- CAUTION: Was thought to be a dihydrodipicolinate synthase (DHDPS),
CC catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-
CC ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown
CC 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 -!- SEQUENCE CAUTION:
CC Sequence=AAA26301.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; L17071; AAA26301.1; ALT_FRAME; Genomic_DNA.
DR PIR; B53308; B53308.
DR RefSeq; WP_032490783.1; NZ_JZXD01000015.1.
DR PDB; 2VC6; X-ray; 1.95 A; A/B=1-292.
DR PDBsum; 2VC6; -.
DR AlphaFoldDB; Q07607; -.
DR SMR; Q07607; -.
DR PATRIC; fig|382.53.peg.1542; -.
DR BRENDA; 4.3.3.7; 5347.
DR UniPathway; UPA00034; UER00017.
DR EvolutionaryTrace; Q07607; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008840; F:4-hydroxy-tetrahydrodipicolinate synthase activity; IEA:UniProtKB-UniRule.
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; Allosteric enzyme; Amino-acid biosynthesis; Cytoplasm;
KW Diaminopimelate biosynthesis; Lyase; Lysine biosynthesis; Plasmid;
KW Schiff base.
FT CHAIN 1..292
FT /note="4-hydroxy-tetrahydrodipicolinate synthase"
FT /id="PRO_0000103228"
FT ACT_SITE 132
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:18536061"
FT ACT_SITE 161
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418,
FT ECO:0000269|PubMed:18536061"
FT BINDING 44
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT BINDING 203
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:0000305"
FT SITE 106
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000305"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 20..32
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 36..39
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 52..66
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 72..75
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 81..93
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 111..124
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 144..153
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 168..176
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 181..186
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 191..196
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 211..222
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 226..242
FT /evidence="ECO:0007829|PDB:2VC6"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 250..258
FT /evidence="ECO:0007829|PDB:2VC6"
FT HELIX 275..287
FT /evidence="ECO:0007829|PDB:2VC6"
SQ SEQUENCE 292 AA; 31310 MW; 47E74D7A282C3640 CRC64;
MFEGSITALV TPFADDRIDE VALHDLVEWQ IEEGSFGLVP CGTTGESPTL SKSEHEQVVE
ITIKTANGRV PVIAGAGSNS TAEAIAFVRH AQNAGADGVL IVSPYYNKPT QEGIYQHFKA
IDAASTIPII VYNIPGRSAI EIHVETLARI FEDCPNVKGV KDATGNLLRP SLERMACGED
FNLLTGEDGT ALGYMAHGGH GCISVTANVA PALCADFQQA CLNGDFAAAL KLQDRLMPLH
RALFLETNPA GAKYALQRLG RMRGDLRLPL VTISPSFQEE IDDAMRHAGI LL
