DAPA_STAAC
ID DAPA_STAAC Reviewed; 295 AA.
AC Q5HG25;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 107.
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=SACOL1430;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP PYRUVATE, FUNCTION, KINETIC PARAMETERS, ACTIVITY REGULATION, ACTIVE SITES,
RP SITES, AND SUBUNIT.
RC STRAIN=COL;
RX PubMed=18671976; DOI=10.1016/j.febslet.2008.07.035;
RA Girish T.S., Sharma E., Gopal B.;
RT "Structural and functional characterization of Staphylococcus aureus
RT dihydrodipicolinate synthase.";
RL FEBS Lett. 582:2923-2930(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:18671976}.
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 not feedback inhibited by lysine.
CC {ECO:0000269|PubMed:18671976}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.12 mM for pyruvate {ECO:0000269|PubMed:18671976};
CC KM=0.33 mM for L-aspartate-4-semialdehyde
CC {ECO:0000269|PubMed:18671976};
CC Vmax=5.3 umol/sec/mg enzyme {ECO:0000269|PubMed:18671976};
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:18671976}.
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; CP000046; AAW38175.1; -; Genomic_DNA.
DR RefSeq; WP_000149257.1; NC_002951.2.
DR PDB; 3DI0; X-ray; 2.38 A; A/B=1-295.
DR PDB; 3DI1; X-ray; 2.20 A; A/B=1-295.
DR PDBsum; 3DI0; -.
DR PDBsum; 3DI1; -.
DR AlphaFoldDB; Q5HG25; -.
DR SMR; Q5HG25; -.
DR EnsemblBacteria; AAW38175; AAW38175; SACOL1430.
DR KEGG; sac:SACOL1430; -.
DR HOGENOM; CLU_049343_7_0_9; -.
DR OMA; GMDACVP; -.
DR BRENDA; 4.3.3.7; 3352.
DR SABIO-RK; Q5HG25; -.
DR UniPathway; UPA00034; UER00017.
DR EvolutionaryTrace; Q5HG25; -.
DR Proteomes; UP000000530; Chromosome.
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 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; PS00666; DHDPS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cytoplasm;
KW Diaminopimelate biosynthesis; Lyase; Lysine biosynthesis; Schiff base.
FT CHAIN 1..295
FT /note="4-hydroxy-tetrahydrodipicolinate synthase"
FT /id="PRO_0000103154"
FT ACT_SITE 135
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:18671976"
FT ACT_SITE 163
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418,
FT ECO:0000269|PubMed:18671976"
FT BINDING 47
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418,
FT ECO:0000269|PubMed:18671976"
FT BINDING 206
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT SITE 46
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000305"
FT SITE 109
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000305"
FT STRAND 6..11
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 23..35
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 39..45
FT /evidence="ECO:0007829|PDB:3DI1"
FT TURN 46..49
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 55..69
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 84..97
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 100..105
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 114..128
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 138..141
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 147..154
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 169..176
FT /evidence="ECO:0007829|PDB:3DI1"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 184..189
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 194..199
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 214..225
FT /evidence="ECO:0007829|PDB:3DI1"
FT TURN 231..234
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 235..244
FT /evidence="ECO:0007829|PDB:3DI1"
FT TURN 249..252
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 253..259
FT /evidence="ECO:0007829|PDB:3DI1"
FT STRAND 262..265
FT /evidence="ECO:0007829|PDB:3DI1"
FT HELIX 276..290
FT /evidence="ECO:0007829|PDB:3DI1"
SQ SEQUENCE 295 AA; 32584 MW; 6ED1E5887F0C2C01 CRC64;
MTHLFEGVGV ALTTPFTNNK VNIEALKTHV NFLLENNAQA IIVNGTTAES PTLTTDEKER
ILKTVIDLVD KRVPVIAGTG TNDTEKSIQA SIQAKALGAD AIMLITPYYN KTNQRGLVKH
FEAIADAVKL PVVLYNVPSR TNMTIEPETV EILSQHPYIV ALKDATNDFE YLEEVKKRID
TNSFALYSGN DDNVVEYYQR GGQGVISVIA NVIPKEFQAL YDAQQSGLDI QDQFKPIGTL
LSALSVDINP IPIKALTSYL GFGNYELRLP LVSLEDTDTK VLRETYDTFK AGENE
