DAPE_SALTY
ID DAPE_SALTY Reviewed; 375 AA.
AC Q8ZN75;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase;
DE Short=SDAP desuccinylase;
DE EC=3.5.1.18;
DE AltName: Full=Aspartyl peptidase;
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase;
GN Name=dapE; OrderedLocusNames=STM2483;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, COFACTOR, AND
RP SUBSTRATE SPECIFICITY.
RX PubMed=12896993; DOI=10.1128/jb.185.16.4748-4754.2003;
RA Broder D.H., Miller C.G.;
RT "DapE can function as an aspartyl peptidase in the presence of Mn2+.";
RL J. Bacteriol. 185:4748-4754(2003).
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. Can also hydrolyze all N-terminal Asp dipeptides except Asp-Pro.
CC Asp-Ser is the best substrate, followed by Asp-Gly, Asp-Leu, and Asp-
CC Cys. {ECO:0000269|PubMed:12896993}.
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;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12896993};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:12896993};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:12896993};
CC Note=Binds 2 divalent cations per subunit, one with high affinity and
CC the other with lower affinity. Zn(2+) and/or Co(2+) ions are used for
CC desuccinylase activity. The form of DapE active as a peptidase contains
CC Zn(2+) in the high-affinity site and Mn(2+) in the low-affinity site.
CC {ECO:0000269|PubMed:12896993};
CC -!- ACTIVITY REGULATION: Mn(2+)-activated peptidase is inhibited by Mn(2+)
CC at concentration above 1 mM and by increasing concnentrations of
CC Co(2+). There is a competitive inhibitor effect between the substrates.
CC Hydrolysis of Asp-Leu by Mn(2+)-activated DapE is inhibited by SDAP,
CC and hydrolysis of SDAP by Co(2+)-activated DapE is inhibited by Asp-
CC Ser. {ECO:0000269|PubMed:12896993}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.63 mM for SDAP (in the presence of 1 mM Co(2+)
CC {ECO:0000269|PubMed:12896993};
CC KM=0.66 mM for Asp-Ser (in the presence of 1 mM Mn(2+)
CC {ECO:0000269|PubMed:12896993};
CC KM=3.3 mM for Asp-Leu (in the presence of 1 mM Mn(2+)
CC {ECO:0000269|PubMed:12896993};
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.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- MISCELLANEOUS: Zn(+2) is usually found in the tight binding site, but
CC the nature of the second cation in the low affinity binding site is
CC different according the activity.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000305}.
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DR EMBL; AE006468; AAL21377.1; -; Genomic_DNA.
DR RefSeq; NP_461418.1; NC_003197.2.
DR RefSeq; WP_001277825.1; NC_003197.2.
DR AlphaFoldDB; Q8ZN75; -.
DR SMR; Q8ZN75; -.
DR STRING; 99287.STM2483; -.
DR MEROPS; M20.010; -.
DR PaxDb; Q8ZN75; -.
DR EnsemblBacteria; AAL21377; AAL21377; STM2483.
DR GeneID; 1254005; -.
DR KEGG; stm:STM2483; -.
DR PATRIC; fig|99287.12.peg.2621; -.
DR HOGENOM; CLU_021802_4_0_6; -.
DR OMA; LNSHHDT; -.
DR PhylomeDB; Q8ZN75; -.
DR BioCyc; SENT99287:STM2483-MON; -.
DR SABIO-RK; Q8ZN75; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016805; F:dipeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0009014; F:succinyl-diaminopimelate desuccinylase activity; IBA:GO_Central.
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:0043093; P:FtsZ-dependent cytokinesis; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
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 1: Evidence at protein level;
KW Amino-acid biosynthesis; Cobalt; Diaminopimelate biosynthesis; Dipeptidase;
KW Hydrolase; Lysine biosynthesis; Manganese; Metal-binding; Metalloprotease;
KW Protease; Reference proteome; Zinc.
FT CHAIN 1..375
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375723"
FT ACT_SITE 68
FT /evidence="ECO:0000250"
FT ACT_SITE 133
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 348
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 375 AA; 41578 MW; ED6165EDEEB262A0 CRC64;
MSCPVIELTQ QLIRRPSLSP DDAGCQALMI ERLRKIGFTI EHMDFGDTQN FWAWRGRGET
LAFAGHTDVV PAGDVDRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAQHPH
HRGRLAFLIT SDEEASAKNG TVKVVEALMA RNERLDYCLV GEPSSTEIVG DVVKNGRRGS
LTCNLTIHGV QGHVAYPHLA DNPVHRAAPF LNELVAIEWD RGNDFFPATS MQVANIQAGT
GSNNVIPGEL FVQFNFRFST ELTDEMIKER VHALLEKHQL RYTVDWWLSG QPFLTARGKL
VDAVVNAIEH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI NECVNAADLQ
LLARMYQRIM EQLVA
