DAPE_RHILO
ID DAPE_RHILO Reviewed; 397 AA.
AC Q98D57;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase {ECO:0000255|HAMAP-Rule:MF_01690};
DE Short=SDAP desuccinylase {ECO:0000255|HAMAP-Rule:MF_01690};
DE EC=3.5.1.18 {ECO:0000255|HAMAP-Rule:MF_01690};
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase {ECO:0000255|HAMAP-Rule:MF_01690};
GN Name=dapE {ECO:0000255|HAMAP-Rule:MF_01690}; OrderedLocusNames=mlr4849;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
CC -!- FUNCTION: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic
CC acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP),
CC an intermediate involved in the bacterial biosynthesis of lysine and
CC meso-diaminopimelic acid, an essential component of bacterial cell
CC walls. {ECO:0000255|HAMAP-Rule:MF_01690}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-
CC 2,6-diaminoheptanedioate + succinate; Xref=Rhea:RHEA:22608,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:30031, ChEBI:CHEBI:57609,
CC ChEBI:CHEBI:58087; EC=3.5.1.18; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01690};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01690};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01690};
CC Note=Binds 2 Zn(2+) or Co(2+) ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_01690};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate
CC (succinylase route): step 3/3. {ECO:0000255|HAMAP-Rule:MF_01690}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01690}.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01690}.
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DR EMBL; BA000012; BAB51414.1; -; Genomic_DNA.
DR RefSeq; WP_010912755.1; NC_002678.2.
DR AlphaFoldDB; Q98D57; -.
DR SMR; Q98D57; -.
DR STRING; 266835.14024812; -.
DR EnsemblBacteria; BAB51414; BAB51414; BAB51414.
DR KEGG; mlo:mlr4849; -.
DR PATRIC; fig|266835.9.peg.3831; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_4_0_5; -.
DR OMA; LNSHHDT; -.
DR OrthoDB; 275025at2; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009014; F:succinyl-diaminopimelate desuccinylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc 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 HAMAP; MF_01690; DapE; 1.
DR InterPro; IPR001261; ArgE/DapE_CS.
DR InterPro; IPR036264; Bact_exopeptidase_dim_dom.
DR InterPro; IPR005941; DapE_proteobac.
DR InterPro; IPR002933; Peptidase_M20.
DR InterPro; IPR011650; Peptidase_M20_dimer.
DR Pfam; PF07687; M20_dimer; 1.
DR Pfam; PF01546; Peptidase_M20; 1.
DR SUPFAM; SSF55031; SSF55031; 1.
DR TIGRFAMs; TIGR01246; dapE_proteo; 1.
DR PROSITE; PS00758; ARGE_DAPE_CPG2_1; 1.
DR PROSITE; PS00759; ARGE_DAPE_CPG2_2; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis; Cobalt; Diaminopimelate biosynthesis; Hydrolase;
KW Lysine biosynthesis; Metal-binding; Zinc.
FT CHAIN 1..397
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375682"
FT ACT_SITE 76
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT ACT_SITE 141
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 107
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 107
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 170
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 368
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
SQ SEQUENCE 397 AA; 42629 MW; 58D2BAFCAC614834 CRC64;
MTLPTDPAAN LAALIRCASV TPAEGGALGA LETMLKPLGF LVDRPVFSED GTPDIENLYA
RRSGNGPHLM FAGHTDVVPV GDEAAWTHPP FAAEIANGEM YGRGAVDMKG GIACFVAAIA
RHVENNGGPK GSVSLLITGD EEGPAINGTV KLLEWAASRG EKWDASIVGE PTNPDTLGDM
IKIGRRGSLS GSITVNGRQG HAAYPQLADN PVRGLMGLVD ALLHPVFDKG TKDFQPTNLE
VTSIDVGNPA TNVIPAKATA TFNIRFNDTW TAETVQAEIH NRLDQAAKRK KYRPGKKTPV
DYDLVWRDRP SHVFLTRDDK LVDTLAGSIK AAVGKEPTLS TSGGTSDARF IKDYCPVVEF
GLVGKTMHMV DERVALADLE TLTRIYQRFI EDWFGQG
