DAPA_PSEAE
ID DAPA_PSEAE Reviewed; 292 AA.
AC Q9I4W3; D1MH64;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, 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=PA1010;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS)
RP OF APOENZYME AND IN COMPLEX WITH (S)-LYSINE, FUNCTION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=21396954; DOI=10.1016/j.ijbiomac.2011.03.002;
RA Kaur N., Gautam A., Kumar S., Singh A., Singh N., Sharma S., Sharma R.,
RA Tewari R., Singh T.P.;
RT "Biochemical studies and crystal structure determination of
RT dihydrodipicolinate synthase from Pseudomonas aeruginosa.";
RL Int. J. Biol. Macromol. 48:779-787(2011).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.59 ANGSTROMS).
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RA Schnell R., Sandalova T., Schneider G.;
RT "High resolution structure of DapA (PA1010) from Pseudomonas aeruginosa
RT PAO1.";
RL Submitted (MAR-2011) to the PDB data bank.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS).
RA Kumar M., Kaur N., Kumar S., Sinha M., Kaur P., Sharma S., Singh T.P.;
RT "Structure of dihydrodipicolinate synthase complexed with 3-
RT hydroxypropanoic acid (HPA) at 2.70 A resolution.";
RL Submitted (MAY-2011) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the condensation of (S)-aspartate-beta-semialdehyde
CC [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
CC {ECO:0000305|PubMed:21396954}.
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.90 mM for pyruvate {ECO:0000269|PubMed:21396954};
CC KM=0.17 mM for L-aspartate-4-semialdehyde
CC {ECO:0000269|PubMed:21396954};
CC Vmax=0.030 mmol/min/ug enzyme {ECO:0000269|PubMed:21396954};
CC pH dependence:
CC Optimum pH is 8.0. At pH 9.0 or above, only 30% activity is observed.
CC {ECO:0000269|PubMed:21396954};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius. The activity decreases
CC slowly when temperatures are reduced from 37 degrees Celsius while
CC the drop in activity is relatively more rapid when temperatures are
CC raised above 37 degrees Celsius. In this case, the activity reduces
CC to almost 30% at 52 degrees Celsius. {ECO:0000269|PubMed:21396954};
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: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00418,
CC ECO:0000269|PubMed:21396954}.
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; GU166748; ACZ37227.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG04399.1; -; Genomic_DNA.
DR PIR; C83520; C83520.
DR RefSeq; NP_249701.1; NC_002516.2.
DR RefSeq; WP_003086270.1; NZ_QZGE01000006.1.
DR PDB; 3NOE; X-ray; 2.95 A; A/B=1-292.
DR PDB; 3PS7; X-ray; 2.85 A; A/B=1-292.
DR PDB; 3PUO; X-ray; 2.65 A; A/B=1-292.
DR PDB; 3QZE; X-ray; 1.59 A; A/B/C/D=1-292.
DR PDB; 3S8H; X-ray; 2.70 A; A/B=1-292.
DR PDB; 6P90; X-ray; 1.90 A; A/B=1-292.
DR PDBsum; 3NOE; -.
DR PDBsum; 3PS7; -.
DR PDBsum; 3PUO; -.
DR PDBsum; 3QZE; -.
DR PDBsum; 3S8H; -.
DR PDBsum; 6P90; -.
DR AlphaFoldDB; Q9I4W3; -.
DR SMR; Q9I4W3; -.
DR STRING; 287.DR97_937; -.
DR PaxDb; Q9I4W3; -.
DR PRIDE; Q9I4W3; -.
DR EnsemblBacteria; AAG04399; AAG04399; PA1010.
DR GeneID; 879525; -.
DR KEGG; pae:PA1010; -.
DR PATRIC; fig|208964.12.peg.1042; -.
DR PseudoCAP; PA1010; -.
DR HOGENOM; CLU_049343_7_1_6; -.
DR InParanoid; Q9I4W3; -.
DR OMA; GMDACVP; -.
DR PhylomeDB; Q9I4W3; -.
DR BioCyc; PAER208964:G1FZ6-1029-MON; -.
DR BRENDA; 4.3.3.7; 5087.
DR UniPathway; UPA00034; UER00017.
DR EvolutionaryTrace; Q9I4W3; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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..292
FT /note="4-hydroxy-tetrahydrodipicolinate synthase"
FT /id="PRO_0000103138"
FT ACT_SITE 133
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 45
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 44
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT SITE 107
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT CONFLICT 234
FT /note="D -> E (in Ref. 1; ACZ37227)"
FT /evidence="ECO:0000305"
FT CONFLICT 276
FT /note="R -> H (in Ref. 1; ACZ37227)"
FT /evidence="ECO:0000305"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 21..34
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 53..67
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 82..94
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:3QZE"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:3PS7"
FT HELIX 112..125
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 130..134
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 136..139
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 145..152
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 167..176
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 181..186
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 191..196
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 211..222
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 226..242
FT /evidence="ECO:0007829|PDB:3QZE"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 250..258
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 275..277
FT /evidence="ECO:0007829|PDB:3QZE"
FT HELIX 278..287
FT /evidence="ECO:0007829|PDB:3QZE"
SQ SEQUENCE 292 AA; 31449 MW; 8E611F4C2A4A60FE CRC64;
MIAGSMVALV TPFDAQGRLD WDSLAKLVDF HLQEGTNAIV AVGTTGESAT LDVEEHIQVI
RRVVDQVKGR IPVIAGTGAN STREAVALTE AAKSGGADAC LLVTPYYNKP TQEGMYQHFR
HIAEAVAIPQ ILYNVPGRTS CDMLPETVER LSKVPNIIGI KEATGDLQRA KEVIERVGKD
FLVYSGDDAT AVELMLLGGK GNISVTANVA PRAMSDLCAA AMRGDAAAAR AINDRLMPLH
KALFIESNPI PVKWALHEMG LIPEGIRLPL TWLSPRCHEP LRQAMRQTGV LA
