DAPA_AGRFC
ID DAPA_AGRFC Reviewed; 294 AA.
AC Q8UGL3;
DT 19-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 115.
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};
GN Synonyms=dapA7 {ECO:0000303|PubMed:24677246}; OrderedLocusNames=Atu1024;
GN ORFNames=AGR_C_1883;
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(2001).
RN [3]
RP CRYSTALLIZATION.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=22949190; DOI=10.1107/s1744309112033052;
RA Atkinson S.C., Dogovski C., Dobson R.C., Perugini M.A.;
RT "Cloning, expression, purification and crystallization of
RT dihydrodipicolinate synthase from Agrobacterium tumefaciens.";
RL Acta Crystallogr. F 68:1040-1047(2012).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP PYRUVATE AND LYSINE INHIBITOR, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES,
RP ACTIVITY REGULATION, SUBUNIT, AND ACTIVE SITE.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=24677246; DOI=10.1002/prot.24539;
RA Atkinson S.C., Hor L., Dogovski C., Dobson R.C., Perugini M.A.;
RT "Identification of the bona fide DHDPS from a common plant pathogen.";
RL Proteins 82:1869-1883(2014).
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, ECO:0000305|PubMed:24677246}.
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 allosterically regulated by the feedback
CC inhibitor (S)-lysine. {ECO:0000269|PubMed:24677246}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.31 mM for pyruvate {ECO:0000269|PubMed:24677246};
CC KM=0.32 mM for L-aspartate-4-semialdehyde
CC {ECO:0000269|PubMed:24677246};
CC Vmax=26 umol/min/mg enzyme {ECO:0000269|PubMed:24677246};
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:24677246}.
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: The DapA family was originally thought to be
CC dihydrodipicolinate synthases (DHDPS), catalyzing the condensation of
CC (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to
CC dihydrodipicolinate (DHDP). However, it was shown in E.coli that the
CC product of the enzymatic reaction is not dihydrodipicolinate but in
CC fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA),
CC and that the consecutive dehydration reaction leading to DHDP is not
CC spontaneous but catalyzed by DapB. This enzyme is still named DHDPS in
CC PubMed:22949190 and PubMed:24677246, but since DHDPS is considered as a
CC misleading name, it was not used in this entry. {ECO:0000305}.
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DR EMBL; AE007869; AAK86832.1; -; Genomic_DNA.
DR PIR; AG2702; AG2702.
DR PIR; G97484; G97484.
DR RefSeq; NP_354047.1; NC_003062.2.
DR RefSeq; WP_006311526.1; NC_003062.2.
DR PDB; 4I7U; X-ray; 1.55 A; A/B/C/D=1-294.
DR PDB; 4I7V; X-ray; 1.45 A; A/B/C/D=1-294.
DR PDB; 4I7W; X-ray; 1.30 A; A/B=1-294.
DR PDBsum; 4I7U; -.
DR PDBsum; 4I7V; -.
DR PDBsum; 4I7W; -.
DR AlphaFoldDB; Q8UGL3; -.
DR SMR; Q8UGL3; -.
DR STRING; 176299.Atu1024; -.
DR EnsemblBacteria; AAK86832; AAK86832; Atu1024.
DR KEGG; atu:Atu1024; -.
DR PATRIC; fig|176299.10.peg.1037; -.
DR eggNOG; COG0329; Bacteria.
DR HOGENOM; CLU_049343_7_0_5; -.
DR OMA; GMDACVP; -.
DR PhylomeDB; Q8UGL3; -.
DR BioCyc; AGRO:ATU1024-MON; -.
DR BRENDA; 4.3.3.7; 200.
DR SABIO-RK; Q8UGL3; -.
DR UniPathway; UPA00034; UER00017.
DR Proteomes; UP000000813; Chromosome circular.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008840; F:4-hydroxy-tetrahydrodipicolinate synthase activity; IDA:UniProtKB.
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 GO; GO:0006090; P:pyruvate metabolic process; IDA:UniProtKB.
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;
KW Reference proteome; Schiff base.
FT CHAIN 1..294
FT /note="4-hydroxy-tetrahydrodipicolinate synthase"
FT /id="PRO_0000103079"
FT ACT_SITE 133
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
FT ACT_SITE 162
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418,
FT ECO:0000269|PubMed:24677246"
FT BINDING 45
FT /ligand="pyruvate"
FT /ligand_id="ChEBI:CHEBI:15361"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418,
FT ECO:0000269|PubMed:24677246"
FT BINDING 204
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 49
FT /note="L-lysine inhibitor binding; via carbonyl oxygen"
FT /evidence="ECO:0000269|PubMed:24677246"
FT SITE 56
FT /note="L-lysine inhibitor binding"
FT /evidence="ECO:0000269|PubMed:24677246"
FT SITE 80
FT /note="L-lysine inhibitor binding"
FT /evidence="ECO:0000269|PubMed:24677246"
FT SITE 84
FT /note="L-lysine inhibitor binding"
FT /evidence="ECO:0000269|PubMed:24677246"
FT SITE 106
FT /note="L-lysine inhibitor binding"
FT /evidence="ECO:0000269|PubMed:24677246"
FT SITE 107
FT /note="Part of a proton relay during catalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00418"
SQ SEQUENCE 294 AA; 31133 MW; 9268D7C3B21120A7 CRC64;
MFKGSIPALI TPFTDNGSVD EKAFAAHVEW QIAEGSNGLV PVGTTGESPT LSHDEHKRVV
ELCIEVAAKR VPVIAGAGSN NTDEAIELAL HAQEAGADAL LVVTPYYNKP TQKGLFAHFS
AVAEAVKLPI VIYNIPPRSV VDMSPETMGA LVKAHKNIIG VKDATGKLDR VSEQRISCGK
DFVQLSGEDG TALGFNAHGG VGCISVTANV APRLCSEFQA AMLAGDYAKA LEYQDRLMPL
HRAIFMEPGV CGTKYALSKT RGGNRRVRSP LMSTLEPATE AAIDAALKHA GLMN
