DAPE_SHIFL
ID DAPE_SHIFL Reviewed; 375 AA.
AC P0AED8; P24176;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 114.
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};
GN OrderedLocusNames=SF2514, S2665;
OS Shigella flexneri.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700930 / 2457T / Serotype 2a;
RX PubMed=12704152; DOI=10.1128/iai.71.5.2775-2786.2003;
RA Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G.,
RA Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T.,
RA Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.;
RT "Complete genome sequence and comparative genomics of Shigella flexneri
RT serotype 2a strain 2457T.";
RL Infect. Immun. 71:2775-2786(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. {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; AE005674; AAN44017.1; -; Genomic_DNA.
DR EMBL; AE014073; AAP17832.1; -; Genomic_DNA.
DR RefSeq; NP_708310.1; NC_004337.2.
DR RefSeq; WP_001277801.1; NZ_WPGW01000011.1.
DR PDB; 7LGP; X-ray; 1.91 A; A/B=1-375.
DR PDBsum; 7LGP; -.
DR AlphaFoldDB; P0AED8; -.
DR SMR; P0AED8; -.
DR STRING; 198214.SF2514; -.
DR MEROPS; M20.010; -.
DR EnsemblBacteria; AAN44017; AAN44017; SF2514.
DR EnsemblBacteria; AAP17832; AAP17832; S2665.
DR GeneID; 1025615; -.
DR GeneID; 66673666; -.
DR KEGG; sfl:SF2514; -.
DR KEGG; sfx:S2665; -.
DR PATRIC; fig|198214.7.peg.3006; -.
DR HOGENOM; CLU_021802_4_0_6; -.
DR OMA; LNSHHDT; -.
DR OrthoDB; 275025at2; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000001006; Chromosome.
DR Proteomes; UP000002673; 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 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cobalt;
KW Diaminopimelate biosynthesis; Hydrolase; Lysine biosynthesis;
KW Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..375
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000185263"
FT ACT_SITE 68
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT ACT_SITE 133
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 348
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT HELIX 4..14
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 25..34
FT /evidence="ECO:0007829|PDB:7LGP"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 50..66
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:7LGP"
FT TURN 95..100
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 101..117
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 122..131
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 141..150
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 179..188
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 203..216
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 230..238
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 248..258
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 264..277
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 282..290
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 299..312
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 317..319
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 327..330
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 331..333
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 336..339
FT /evidence="ECO:0007829|PDB:7LGP"
FT TURN 345..348
FT /evidence="ECO:0007829|PDB:7LGP"
FT STRAND 353..355
FT /evidence="ECO:0007829|PDB:7LGP"
FT HELIX 356..374
FT /evidence="ECO:0007829|PDB:7LGP"
SQ SEQUENCE 375 AA; 41269 MW; 181F43D05E88C20E CRC64;
MSCPVIELTQ QLIRRPSLSP DDAGCQALLI ERLQAIGFTV ERMDFADTQN FWAWRGQGET
LAFAGHTDVV PPGDADRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAQHPN
HTGRLAFLIT SDEEASAHNG TVKVVEALMA RNERLDYCLV GEPSSIEVVG DVVKNGRRGS
LTCNLTIHGV QGHVAYPHLA DNPVHRAAPF LNELVAIEWD QGNEFFPATS MQIANIQAGT
GSNNVIPGEL FVQFNFRFST ELTDEMIKAQ VLALLEKHQL RYTVDWWLSG QPFLTARGKL
VDAVVNAVEH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI NECVNAADLQ
LLARMYQRIM EQLVA
