DAPD_UNKP
ID DAPD_UNKP Reviewed; 274 AA.
AC P56220;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-1998, sequence version 2.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase;
DE EC=2.3.1.117;
DE AltName: Full=Tetrahydrodipicolinate N-succinyltransferase;
DE Short=THDP succinyltransferase;
DE Short=THP succinyltransferase;
DE Short=Tetrahydropicolinate succinylase;
GN Name=dapD;
OS Unknown prokaryotic organism.
OC Bacteria; environmental samples.
OX NCBI_TaxID=2725;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CRYSTALLIZATION.
RX PubMed=8880935;
RX DOI=10.1002/(sici)1097-0134(199609)26:1<115::aid-prot11>3.0.co;2-j;
RA Binder D.A., Blanchard J.S., Roderick S.L.;
RT "Crystallization and preliminary crystallographic analysis of
RT tetrahydrodipicolinate-N-succinyltransferase.";
RL Proteins 26:115-117(1996).
RN [2]
RP DISCUSSION OF ORIGIN OF SEQUENCE.
RX PubMed=19394346; DOI=10.1016/j.jmb.2009.04.046;
RA Schuldt L., Weyand S., Kefala G., Weiss M.S.;
RT "The three-dimensional structure of a mycobacterial DapD provides insights
RT into DapD diversity and reveals unexpected particulars about the enzymatic
RT mechanism.";
RL J. Mol. Biol. 389:863-879(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=9012664; DOI=10.1021/bi962522q;
RA Beaman T.W., Binder D.A., Blanchard J.S., Roderick S.L.;
RT "Three-dimensional structure of tetrahydrodipicolinate N-
RT succinyltransferase.";
RL Biochemistry 36:489-494(1997).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH ANALOGS SUBSTRATE.
RX PubMed=9671504; DOI=10.1021/bi980759b;
RA Beaman T.W., Blanchard J.S., Roderick S.L.;
RT "The conformational change and active site structure of
RT tetrahydrodipicolinate N-succinyltransferase.";
RL Biochemistry 37:10363-10369(1998).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH ANALOGS SUBSTRATES.
RX PubMed=11910040; DOI=10.1110/ps.4310102;
RA Beaman T.W., Vogel K.W., Drueckhammer D.G., Blanchard J.S., Roderick S.L.;
RT "Acyl group specificity at the active site of tetrahydrodipicolinate N-
RT succinyltransferase.";
RL Protein Sci. 11:974-979(2002).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = (S)-
CC 2-succinylamino-6-oxoheptanedioate + CoA; Xref=Rhea:RHEA:17325,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15685, ChEBI:CHEBI:16845,
CC ChEBI:CHEBI:57287, ChEBI:CHEBI:57292; EC=2.3.1.117;
CC -!- ACTIVITY REGULATION: Inhibited by p-(chloromercuri)benzenesulfonic acid
CC and cobalt. {ECO:0000269|PubMed:9012664}.
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate
CC (succinylase route): step 1/3.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:9012664}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the transferase hexapeptide repeat family.
CC {ECO:0000305}.
CC -!- CAUTION: Was originally thought to originate from Mycobacterium bovis
CC (PubMed:8880935, PubMed:9012664, PubMed:9671504 and PubMed:11910040).
CC However, there is now convincing evidence that this is incorrect
CC (PubMed:19394346). The source is unknown, but the sequence similarity
CC suggests the protein is of enterobacterial origin.
CC {ECO:0000305|PubMed:19394346}.
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DR PDB; 1KGQ; X-ray; 2.00 A; A=1-274.
DR PDB; 1KGT; X-ray; 2.30 A; A=1-274.
DR PDB; 1TDT; X-ray; 2.20 A; A/B/C=1-259.
DR PDB; 2TDT; X-ray; 2.00 A; A=1-274.
DR PDB; 3TDT; X-ray; 2.00 A; A=1-274.
DR PDBsum; 1KGQ; -.
DR PDBsum; 1KGT; -.
DR PDBsum; 1TDT; -.
DR PDBsum; 2TDT; -.
DR PDBsum; 3TDT; -.
DR AlphaFoldDB; P56220; -.
DR SMR; P56220; -.
DR DrugBank; DB01992; Coenzyme A.
DR DrugBank; DB03134; L-2-aminopimelic acid.
DR DrugBank; DB01856; Pimelic Acid.
DR DrugBank; DB03905; Succinamide-CoA.
DR DrugBank; DB03699; Succinyl-Coenzyme A.
DR PRIDE; P56220; -.
DR UniPathway; UPA00034; UER00019.
DR EvolutionaryTrace; P56220; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008666; F:2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase 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-UniRule.
DR Gene3D; 1.10.166.10; -; 1.
DR HAMAP; MF_00811; DapD; 1.
DR InterPro; IPR005664; DapD_Trfase_Hexpep_rpt_fam.
DR InterPro; IPR001451; Hexapep.
DR InterPro; IPR018357; Hexapep_transf_CS.
DR InterPro; IPR023180; THP_succinylTrfase_dom1.
DR InterPro; IPR037133; THP_succinylTrfase_N_sf.
DR InterPro; IPR011004; Trimer_LpxA-like_sf.
DR Pfam; PF00132; Hexapep; 1.
DR Pfam; PF14602; Hexapep_2; 1.
DR Pfam; PF14805; THDPS_N_2; 1.
DR SUPFAM; SSF51161; SSF51161; 1.
DR TIGRFAMs; TIGR00965; dapD; 1.
DR PROSITE; PS00101; HEXAPEP_TRANSFERASES; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acyltransferase; Amino-acid biosynthesis; Cytoplasm;
KW Diaminopimelate biosynthesis; Lysine biosynthesis; Repeat; Transferase.
FT CHAIN 1..274
FT /note="2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
FT succinyltransferase"
FT /id="PRO_0000196949"
FT BINDING 104
FT /ligand="substrate"
FT BINDING 141
FT /ligand="substrate"
FT HELIX 2..13
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:1KGQ"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 25..39
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 57..69
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 78..86
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 89..92
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 110..112
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:1KGQ"
FT TURN 168..171
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:1KGQ"
FT TURN 217..219
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:1TDT"
FT STRAND 225..227
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 231..239
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:1KGQ"
FT STRAND 246..255
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 258..264
FT /evidence="ECO:0007829|PDB:1KGQ"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:1KGQ"
SQ SEQUENCE 274 AA; 29887 MW; B1F54AE159C13278 CRC64;
MQQLQNVIES AFERRADITP ANVDTVTREA VNQVIGLLDS GALRVAEKID GQWVTHQWLK
KAVLLSFRIN DNKVMDGAET RYYDKVPMKF ADYDEARFQK EGFRVVPPAT VRQGAFIARN
TVLMPSYVNI GAYVDEGTMV DTWATVGSCA QIGKNVHLSG GVGIGGVLEP LQANPTIIED
NCFIGARSEV VEGVIVEEGS VISMGVYLGQ STRIYDRETG EIHYGRVPAG SVVVSGNLPS
KDGSYSLYCA VIVKKVDAKT RGKVGINELL RTID
