DAPD_CORGL
ID DAPD_CORGL Reviewed; 297 AA.
AC Q8NRE3; Q6M660;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase {ECO:0000255|HAMAP-Rule:MF_02122};
DE EC=2.3.1.117 {ECO:0000255|HAMAP-Rule:MF_02122};
DE AltName: Full=Tetrahydrodipicolinate N-succinyltransferase {ECO:0000255|HAMAP-Rule:MF_02122};
DE Short=THDP succinyltransferase {ECO:0000255|HAMAP-Rule:MF_02122};
DE Short=THP succinyltransferase {ECO:0000255|HAMAP-Rule:MF_02122};
DE AltName: Full=Tetrahydropicolinate succinylase {ECO:0000255|HAMAP-Rule:MF_02122};
GN Name=dapD {ECO:0000255|HAMAP-Rule:MF_02122};
GN OrderedLocusNames=Cgl1106, cg1256;
OS Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 /
OS JCM 1318 / LMG 3730 / NCIMB 10025).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=196627;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12743753; DOI=10.1007/s00253-003-1328-1;
RA Ikeda M., Nakagawa S.;
RT "The Corynebacterium glutamicum genome: features and impacts on
RT biotechnological processes.";
RL Appl. Microbiol. Biotechnol. 62:99-109(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12948626; DOI=10.1016/s0168-1656(03)00154-8;
RA Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A.,
RA Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A.,
RA Hartmann M., Huthmacher K., Kraemer R., Linke B., McHardy A.C., Meyer F.,
RA Moeckel B., Pfefferle W., Puehler A., Rey D.A., Rueckert C., Rupp O.,
RA Sahm H., Wendisch V.F., Wiegraebe I., Tauch A.;
RT "The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its
RT impact on the production of L-aspartate-derived amino acids and vitamins.";
RL J. Biotechnol. 104:5-25(2003).
CC -!- FUNCTION: Catalyzes the conversion of the cyclic tetrahydrodipicolinate
CC (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using
CC succinyl-CoA. {ECO:0000255|HAMAP-Rule:MF_02122}.
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 Evidence={ECO:0000255|HAMAP-Rule:MF_02122};
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. {ECO:0000255|HAMAP-Rule:MF_02122}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_02122}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_02122}.
CC -!- SIMILARITY: Belongs to the type 2 tetrahydrodipicolinate N-
CC succinyltransferase family. {ECO:0000255|HAMAP-Rule:MF_02122}.
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DR EMBL; BA000036; BAB98499.1; -; Genomic_DNA.
DR EMBL; BX927151; CAF19812.1; -; Genomic_DNA.
DR RefSeq; NP_600334.1; NC_003450.3.
DR RefSeq; WP_003863790.1; NC_006958.1.
DR PDB; 5E3P; X-ray; 2.01 A; A=2-297.
DR PDB; 5E3Q; X-ray; 1.80 A; A=2-297.
DR PDB; 5E3R; X-ray; 1.85 A; A=2-297.
DR PDBsum; 5E3P; -.
DR PDBsum; 5E3Q; -.
DR PDBsum; 5E3R; -.
DR AlphaFoldDB; Q8NRE3; -.
DR SMR; Q8NRE3; -.
DR STRING; 196627.cg1256; -.
DR KEGG; cgb:cg1256; -.
DR KEGG; cgl:Cgl1106; -.
DR PATRIC; fig|196627.13.peg.1085; -.
DR eggNOG; COG2171; Bacteria.
DR HOGENOM; CLU_057490_1_0_11; -.
DR OMA; TVLDTWF; -.
DR BRENDA; 2.3.1.117; 960.
DR UniPathway; UPA00034; UER00019.
DR Proteomes; UP000000582; Chromosome.
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:0000287; F:magnesium ion binding; 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; 3.30.60.70; -; 1.
DR HAMAP; MF_02122; DapD_type2; 1.
DR InterPro; IPR019875; DapD_actinobacteria.
DR InterPro; IPR001451; Hexapep.
DR InterPro; IPR032784; THDPS_M.
DR InterPro; IPR038361; THDPS_M_sf.
DR InterPro; IPR011004; Trimer_LpxA-like_sf.
DR InterPro; IPR026586; Type2_DapD.
DR Pfam; PF14602; Hexapep_2; 1.
DR Pfam; PF14789; THDPS_M; 1.
DR SUPFAM; SSF51161; SSF51161; 1.
DR TIGRFAMs; TIGR03535; DapD_actino; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acyltransferase; Amino-acid biosynthesis; Cytoplasm;
KW Diaminopimelate biosynthesis; Lysine biosynthesis; Magnesium;
KW Metal-binding; Reference proteome; Transferase.
FT CHAIN 1..297
FT /note="2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
FT succinyltransferase"
FT /id="PRO_0000412258"
FT ACT_SITE 181
FT /note="Acyl-anhydride intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 148
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="ligand shared between trimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 165
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="ligand shared between trimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 183
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 198
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 201
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 224
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 239..240
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 247
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 258
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 271..274
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT STRAND 3..13
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 18..22
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 24..27
FT /evidence="ECO:0007829|PDB:5E3Q"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 39..41
FT /evidence="ECO:0007829|PDB:5E3Q"
FT TURN 42..45
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 46..56
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 64..75
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 89..92
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 102..106
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 109..116
FT /evidence="ECO:0007829|PDB:5E3Q"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 172..176
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:5E3P"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:5E3P"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:5E3Q"
FT HELIX 259..262
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 266..272
FT /evidence="ECO:0007829|PDB:5E3Q"
FT TURN 274..276
FT /evidence="ECO:0007829|PDB:5E3Q"
FT STRAND 279..283
FT /evidence="ECO:0007829|PDB:5E3Q"
SQ SEQUENCE 297 AA; 31170 MW; E0E5258901E42411 CRC64;
MTTASATGIA TLTSTGDVLD VWYPEIGSTD QSALTPLEGV DEDRNVTRKI VTTTIDTDAA
PTDTYDAWLR LHLLSHRVFR PHTINLDGIF GLLNNVVWTN FGPCAVDGFA LTRARLSRRG
QVTVYSVDKF PRMVDYVVPS GVRIGDADRV RLGAYLADGT TVMHEGFVNF NAGTLGASMV
EGRISAGVTV DDGTDVGGGA SIMGTLSGGG QHVISLGKRC LLGANSGCGI PLGDDCIIEA
GLYITAGTKV LFDGSLHKAS TLAGSNGLIF RRDSVSGQVV AVPNTKVVEL NTALHSN
