DAPD_YERPE
ID DAPD_YERPE Reviewed; 274 AA.
AC Q8ZH69; Q0WI04; Q74S45; Q8CZY9;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase {ECO:0000255|HAMAP-Rule:MF_00811};
DE EC=2.3.1.117 {ECO:0000255|HAMAP-Rule:MF_00811};
DE AltName: Full=Tetrahydrodipicolinate N-succinyltransferase {ECO:0000255|HAMAP-Rule:MF_00811};
DE Short=THDP succinyltransferase {ECO:0000255|HAMAP-Rule:MF_00811};
DE Short=THP succinyltransferase {ECO:0000255|HAMAP-Rule:MF_00811};
DE Short=Tetrahydropicolinate succinylase {ECO:0000255|HAMAP-Rule:MF_00811};
GN Name=dapD {ECO:0000255|HAMAP-Rule:MF_00811};
GN OrderedLocusNames=YPO1041, y3140, YP_2810;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
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_00811};
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_00811}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00811}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00811}.
CC -!- SIMILARITY: Belongs to the transferase hexapeptide repeat family.
CC {ECO:0000255|HAMAP-Rule:MF_00811}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM86690.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=AAS62994.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AL590842; CAL19706.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM86690.1; ALT_INIT; Genomic_DNA.
DR EMBL; AE017042; AAS62994.1; ALT_INIT; Genomic_DNA.
DR PIR; AH0127; AH0127.
DR RefSeq; WP_002212128.1; NZ_WUCM01000044.1.
DR RefSeq; YP_002346084.1; NC_003143.1.
DR PDB; 3GOS; X-ray; 1.80 A; A/B/C=1-274.
DR PDBsum; 3GOS; -.
DR AlphaFoldDB; Q8ZH69; -.
DR SMR; Q8ZH69; -.
DR IntAct; Q8ZH69; 4.
DR STRING; 214092.YPO1041; -.
DR PaxDb; Q8ZH69; -.
DR EnsemblBacteria; AAM86690; AAM86690; y3140.
DR EnsemblBacteria; AAS62994; AAS62994; YP_2810.
DR GeneID; 57977520; -.
DR KEGG; ype:YPO1041; -.
DR KEGG; ypk:y3140; -.
DR KEGG; ypm:YP_2810; -.
DR PATRIC; fig|214092.21.peg.1329; -.
DR eggNOG; COG2171; Bacteria.
DR HOGENOM; CLU_050859_0_1_6; -.
DR OMA; YFPIQKM; -.
DR UniPathway; UPA00034; UER00019.
DR EvolutionaryTrace; Q8ZH69; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; 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:0016779; F:nucleotidyltransferase activity; IBA:GO_Central.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IBA:GO_Central.
DR GO; GO:0009085; P:lysine biosynthetic process; IBA:GO_Central.
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; Reference proteome;
KW Repeat; Transferase.
FT CHAIN 1..274
FT /note="2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
FT succinyltransferase"
FT /id="PRO_0000196978"
FT BINDING 104
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00811"
FT BINDING 141
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00811"
FT HELIX 1..13
FT /evidence="ECO:0007829|PDB:3GOS"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:3GOS"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:3GOS"
FT HELIX 25..39
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:3GOS"
FT HELIX 57..68
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 80..86
FT /evidence="ECO:0007829|PDB:3GOS"
FT TURN 89..92
FT /evidence="ECO:0007829|PDB:3GOS"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 110..112
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:3GOS"
FT TURN 217..219
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 225..227
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 231..239
FT /evidence="ECO:0007829|PDB:3GOS"
FT STRAND 246..255
FT /evidence="ECO:0007829|PDB:3GOS"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:3GOS"
SQ SEQUENCE 274 AA; 29937 MW; 5BA5F77C11D66282 CRC64;
MQQLQNVIET AFERRADITP ANVDTVTREA ITHVIDLLDT GALRVAEKID GQWVTHQWLK
KAVLLSFRIN DNQVMEGAET RYYDKVPMKF AGYDEARFQR EGFRVVPPAT VRKGAFIARN
TVLMPSYVNI GAFVDEGTMV DTWATVGSCA QIGKNVHLSG GVGIGGVLEP LQANPTIIED
NCFVGARSEV VEGVIVEEGS VISMGVFIGQ STRIYDRETG EVHYGRVPAG SVVVSGNLPS
KDGSYSLYCA VIVKKVDAKT RSKVGINELL RTID
