ID A0A317NXC7_9GAMM Unreviewed; 390 AA.
AC A0A317NXC7;
DT 10-OCT-2018, integrated into UniProtKB/TrEMBL.
DT 10-OCT-2018, sequence version 1.
DT 27-MAR-2024, entry version 22.
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=DER72_104157 {ECO:0000313|EMBL:PWV79881.1};
OS Halomonas sp. A11-A.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC Halomonadaceae; Halomonas.
OX NCBI_TaxID=2183985 {ECO:0000313|EMBL:PWV79881.1, ECO:0000313|Proteomes:UP000246506};
RN [1] {ECO:0000313|EMBL:PWV79881.1, ECO:0000313|Proteomes:UP000246506}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=A11-A {ECO:0000313|EMBL:PWV79881.1,
RC ECO:0000313|Proteomes:UP000246506};
RA Wrighton K.;
RT "Subsurface microbial communities from deep shales in Ohio and West
RT Virginia, USA.";
RL Submitted (MAY-2018) 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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PWV79881.1}.
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DR EMBL; QGTM01000004; PWV79881.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A317NXC7; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000246506; 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; 1.10.150.900; -; 1.
DR Gene3D; 3.30.70.360; -; 1.
DR Gene3D; 3.40.630.10; Zn peptidases; 1.
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:SF3; ACETYLORNITHINE DEACETYLASE-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; PS00758; ARGE_DAPE_CPG2_1; 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};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01690}.
FT DOMAIN 184..291
FT /note="Peptidase M20 dimerisation"
FT /evidence="ECO:0000259|Pfam:PF07687"
FT ACT_SITE 76
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT ACT_SITE 142
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 108
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 108
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 171
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 357
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
SQ SEQUENCE 390 AA; 42544 MW; 33785DCDCA70BAB3 CRC64;
MPITDPAGLS PTLQLAFELI RRPSVTPDDL GCQALMIERL AALGFRIERL PFGDVENFWA
TRGHHGPLLA FAGHTDVVPS GPHTRWDYPP FEPCIDDDGM LRGRGAADMK GSLAAMVTAV
ERFVAAHPEH HGRIGFLITS DEEGPAVDGT RAVVEHLRER HERLDYCIVG EPSSTARLGD
VIKNGRRGSL GGVLHIKGLQ GHVAYPHLAR NPIHQALPAL DALTREHWDS GNDFFPATSF
QISNIRAGTG ATNVIPGEVE VVFNFRFSTE VTHEQLRQRT AAILDAHGLD YQLDWTLNGE
PFLTAEGELV EAAVLGVEEV MGHRPELSTS GGTSDGRFIA TLGSQVVELG PLNATIHQVN
ERIRAADLDE LSRVYEAILK RLFINGSARP
//
