DAPD_PSEAE
ID DAPD_PSEAE Reviewed; 344 AA.
AC G3XD76; Q7DCA5; Q9Z9H2;
DT 06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 60.
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}; OrderedLocusNames=PA3666;
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].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RA Nashimoto H.;
RT "P.aeruginosa PAO1.";
RL Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases.
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 (1.80 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP SUCCINATE; COA AND 2-AMINOPIMELATE, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP AND SUBUNIT.
RX PubMed=22359568; DOI=10.1371/journal.pone.0031133;
RA Schnell R., Oehlmann W., Sandalova T., Braun Y., Huck C., Maringer M.,
RA Singh M., Schneider G.;
RT "Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate
RT synthase from Pseudomonas aeruginosa: structure analysis and gene
RT deletion.";
RL PLoS ONE 7:E31133-E31133(2012).
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 (By similarity). Displays succinyl transferase activity
CC with L-2-aminopimelate and succinyl-CoA as substrates
CC (PubMed:22359568). {ECO:0000255|HAMAP-Rule:MF_02122,
CC ECO:0000269|PubMed:22359568}.
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 -!- COFACTOR:
CC Note=Magnesium ions are not essential for catalysis.
CC {ECO:0000269|PubMed:22359568};
CC -!- ACTIVITY REGULATION: Weakly inhibited by D-2-aminopimelate.
CC {ECO:0000269|PubMed:22359568}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7 mM for L-2-aminopimelate {ECO:0000269|PubMed:22359568};
CC Vmax=105 umol/min/mg enzyme {ECO:0000269|PubMed:22359568};
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:0000269|PubMed:22359568}.
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; AB024601; BAA75911.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG07054.1; -; Genomic_DNA.
DR PIR; E83187; E83187.
DR RefSeq; NP_252356.1; NC_002516.2.
DR RefSeq; WP_003113860.1; NZ_QZGE01000001.1.
DR PDB; 3R5A; X-ray; 1.89 A; A/B/C/D/E/F=1-344.
DR PDB; 3R5B; X-ray; 2.51 A; A/B/C/D/E/F=1-344.
DR PDB; 3R5C; X-ray; 2.40 A; A/B/C=1-344.
DR PDB; 3R5D; X-ray; 1.80 A; A/B/C/D/E/F=1-344.
DR PDBsum; 3R5A; -.
DR PDBsum; 3R5B; -.
DR PDBsum; 3R5C; -.
DR PDBsum; 3R5D; -.
DR AlphaFoldDB; G3XD76; -.
DR SMR; G3XD76; -.
DR STRING; 287.DR97_4211; -.
DR World-2DPAGE; 0008:Q9Z9H2; -.
DR PaxDb; G3XD76; -.
DR PRIDE; G3XD76; -.
DR DNASU; 880584; -.
DR EnsemblBacteria; AAG07054; AAG07054; PA3666.
DR GeneID; 880584; -.
DR KEGG; pae:PA3666; -.
DR PATRIC; fig|208964.12.peg.3835; -.
DR PseudoCAP; PA3666; -.
DR HOGENOM; CLU_057490_0_0_6; -.
DR InParanoid; G3XD76; -.
DR OMA; TVLDTWF; -.
DR PhylomeDB; G3XD76; -.
DR BioCyc; PAER208964:G1FZ6-3736-MON; -.
DR UniPathway; UPA00034; UER00019.
DR Proteomes; UP000002438; 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; IPR019876; DapD_gammaproteobac.
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; TIGR03536; DapD_gpp; 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..344
FT /note="2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
FT succinyltransferase"
FT /id="PRO_0000421301"
FT ACT_SITE 221
FT /note="Acyl-anhydride intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="ligand shared between trimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02122"
FT BINDING 223
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 238
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 241
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 264
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 279..280
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 287..289
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 304
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT BINDING 317..320
FT /ligand="succinyl-CoA"
FT /ligand_id="ChEBI:CHEBI:57292"
FT /evidence="ECO:0000305|PubMed:22359568"
FT STRAND 6..15
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 21..28
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 35..45
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 49..56
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 58..68
FT /evidence="ECO:0007829|PDB:3R5D"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 73..83
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 89..96
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 103..114
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 128..131
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 164..170
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 182..186
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 187..189
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 212..220
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 222..224
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 267..270
FT /evidence="ECO:0007829|PDB:3R5C"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 299..304
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 305..308
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:3R5D"
FT TURN 320..322
FT /evidence="ECO:0007829|PDB:3R5D"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:3R5D"
FT HELIX 333..341
FT /evidence="ECO:0007829|PDB:3R5C"
SQ SEQUENCE 344 AA; 35973 MW; CF80600C50A316F2 CRC64;
MSQSLFSLAF GVGTQNRQEA WLEVFYALPL LKPSSEIVAA VAPILGYAAG NQALTFTSQQ
AYQLADALKG IDAAQSALLS RLAESQKPLV ATLLAEDAAP SSTAEAYLKL HLLSHRLVKP
HAVNLSGIFP LLPNVAWTNI GAVDLAELAE LQLEARLKGK LLEVFSVDKF PKMTDYVVPA
GVRIADTARV RLGAYIGEGT TVMHEGFVNF NAGTEGPGMI EGRVSAGVFV GKGSDLGGGC
STMGTLSGGG NIVISVGEGC LIGANAGIGI PLGDRNIVEA GLYITAGTKV ALLDEQNALV
KVVKARDLAG QPDLLFRRNS QNGAVECKTN KTAIELNEAL HAHN
