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Database: UniProt
Entry: A0A1G6XMD8_9PROT
LinkDB: A0A1G6XMD8_9PROT
Original site: A0A1G6XMD8_9PROT 
ID   A0A1G6XMD8_9PROT        Unreviewed;       379 AA.
AC   A0A1G6XMD8;
DT   12-APR-2017, integrated into UniProtKB/TrEMBL.
DT   12-APR-2017, sequence version 1.
DT   24-JAN-2024, entry version 25.
DE   RecName: Full=Succinyl-diaminopimelate desuccinylase {ECO:0000256|ARBA:ARBA00022391, ECO:0000256|HAMAP-Rule:MF_01690};
DE            Short=SDAP desuccinylase {ECO:0000256|HAMAP-Rule:MF_01690};
DE            EC=3.5.1.18 {ECO:0000256|ARBA:ARBA00011921, ECO:0000256|HAMAP-Rule:MF_01690};
DE   AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase {ECO:0000256|ARBA:ARBA00031891, ECO:0000256|HAMAP-Rule:MF_01690};
GN   Name=dapE {ECO:0000256|HAMAP-Rule:MF_01690};
GN   ORFNames=SAMN04488071_1287 {ECO:0000313|EMBL:SDD79212.1};
OS   Kordiimonas lacus.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Kordiimonadales;
OC   Kordiimonadaceae; Kordiimonas.
OX   NCBI_TaxID=637679 {ECO:0000313|EMBL:SDD79212.1, ECO:0000313|Proteomes:UP000183685};
RN   [1] {ECO:0000313|EMBL:SDD79212.1, ECO:0000313|Proteomes:UP000183685}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CGMCC 1.9109 {ECO:0000313|EMBL:SDD79212.1,
RC   ECO:0000313|Proteomes:UP000183685};
RA   de Groot N.N.;
RL   Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
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:0000256|HAMAP-Rule:MF_01690}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate =
CC         (2S,6S)-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;
CC         Evidence={ECO:0000256|ARBA:ARBA00001246, ECO:0000256|HAMAP-
CC         Rule:MF_01690};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01690};
CC       Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01690};
CC       Note=Binds 2 Zn(2+) or Co(2+) ions per subunit. {ECO:0000256|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:0000256|ARBA:ARBA00005130,
CC       ECO:0000256|HAMAP-Rule:MF_01690}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000256|ARBA:ARBA00011738, ECO:0000256|HAMAP-
CC       Rule:MF_01690}.
CC   -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC       {ECO:0000256|ARBA:ARBA00006746, ECO:0000256|HAMAP-Rule:MF_01690}.
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DR   EMBL; FNAK01000003; SDD79212.1; -; Genomic_DNA.
DR   RefSeq; WP_068301576.1; NZ_LRUA01000002.1.
DR   AlphaFoldDB; A0A1G6XMD8; -.
DR   STRING; 637679.GCA_001550055_00967; -.
DR   OrthoDB; 9809784at2; -.
DR   UniPathway; UPA00034; UER00021.
DR   Proteomes; UP000183685; Unassembled WGS sequence.
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   CDD; cd03891; M20_DapE_proteobac; 1.
DR   Gene3D; 3.40.630.10; Zn peptidases; 2.
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   NCBIfam; TIGR01246; dapE_proteo; 1.
DR   PANTHER; PTHR43808; ACETYLORNITHINE DEACETYLASE; 1.
DR   PANTHER; PTHR43808:SF31; DIPEPTIDASE YTJP-RELATED; 1.
DR   Pfam; PF07687; M20_dimer; 1.
DR   Pfam; PF01546; Peptidase_M20; 1.
DR   SUPFAM; SSF55031; Bacterial exopeptidase dimerisation domain; 1.
DR   SUPFAM; SSF53187; Zn-dependent exopeptidases; 1.
DR   PROSITE; PS00759; ARGE_DAPE_CPG2_2; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW   Rule:MF_01690};
KW   Cobalt {ECO:0000256|ARBA:ARBA00023285, ECO:0000256|HAMAP-Rule:MF_01690};
KW   Diaminopimelate biosynthesis {ECO:0000256|ARBA:ARBA00022915,
KW   ECO:0000256|HAMAP-Rule:MF_01690};
KW   Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_01690};
KW   Lysine biosynthesis {ECO:0000256|ARBA:ARBA00023154, ECO:0000256|HAMAP-
KW   Rule:MF_01690};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_01690}; Reference proteome {ECO:0000313|Proteomes:UP000183685};
KW   Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01690}.
FT   DOMAIN          181..287
FT                   /note="Peptidase M20 dimerisation"
FT                   /evidence="ECO:0000259|Pfam:PF07687"
FT   ACT_SITE        75
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   ACT_SITE        139
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   BINDING         73
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   BINDING         106
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   BINDING         106
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   BINDING         140
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   BINDING         168
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT   BINDING         352
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
SQ   SEQUENCE   379 AA;  40868 MW;  5F6876683F0A9E03 CRC64;
     MAGLDPITLS QELIRLESVT PDTGDALDLL AGYLGDMGFK CEKLVFEEEG YAPVPNLYAR
     LGTEAPNFCF AGHTDVVPVG AKDHWTVDPF TAEVRDGQLY GRGASDMKSA IAAFVVAVER
     ALAKGAPKGS ISLLITGDEE GDAVNGTKKV LDWMRERGET IDMCLVGEPT NPTEMGQMIK
     IGRRGSLHGI VTVKGMQGHV AYPHVAKNPI PDLVKVLATL DGPLDDGNDR FQPSNLEIVN
     VHVGNESHNV IPAEAKSRFN VRFNNEFTPE ALRAELTRRM DSAGVDYEID WWLSGDSFLT
     PAGPLSDAVQ QAAHARLGVT PELSTTGGTS DARFIKDMCP VVEFGLVGAT MHKIDEHVAV
     ADIEALTDIY EDVISRLLG
//
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