DAPE_HELPY
ID DAPE_HELPY Reviewed; 383 AA.
AC O25002; O32633;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 118.
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=HP_0212;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=ATCC 49503 / 60190;
RX PubMed=9317022; DOI=10.1128/iai.65.10.4158-4164.1997;
RA Karita M., Etterbeek M.L., Forsyth M.H., Tummuru M.K.R., Blaser M.J.;
RT "Characterization of Helicobacter pylori dapE and construction of a
RT conditionally lethal dapE mutant.";
RL Infect. Immun. 65:4158-4164(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
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, ECO:0000269|PubMed:9317022}.
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; AF008565; AAB63297.1; -; Genomic_DNA.
DR EMBL; AE000511; AAD07280.1; -; Genomic_DNA.
DR PIR; D64546; D64546.
DR RefSeq; NP_207010.1; NC_000915.1.
DR RefSeq; WP_000339189.1; NC_018939.1.
DR AlphaFoldDB; O25002; -.
DR SMR; O25002; -.
DR DIP; DIP-3691N; -.
DR IntAct; O25002; 1.
DR MINT; O25002; -.
DR STRING; 85962.C694_01065; -.
DR PaxDb; O25002; -.
DR EnsemblBacteria; AAD07280; AAD07280; HP_0212.
DR KEGG; hpy:HP_0212; -.
DR PATRIC; fig|85962.47.peg.229; -.
DR eggNOG; COG0624; Bacteria.
DR OMA; LNSHHDT; -.
DR PhylomeDB; O25002; -.
DR BRENDA; 3.5.1.18; 2604.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0008777; F:acetylornithine deacetylase activity; IBA:GO_Central.
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:0006526; P:arginine biosynthetic process; IBA:GO_Central.
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; PS00759; ARGE_DAPE_CPG2_2; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis; Cobalt; Diaminopimelate biosynthesis; Hydrolase;
KW Lysine biosynthesis; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..383
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375586"
FT ACT_SITE 81
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 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 110
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 110
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 355
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT CONFLICT 2
FT /note="D -> N (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 33
FT /note="H -> A (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 58
FT /note="D -> EHAEKE (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 61
FT /note="E -> K (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 69
FT /note="T -> V (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 75
FT /note="C -> S (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 87..88
FT /note="NH -> DN (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 97
FT /note="V -> I (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 150
FT /note="R -> K (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 192
FT /note="K -> R (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 221
FT /note="L -> S (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 226
FT /note="N -> H (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 229
FT /note="N -> D (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 241
FT /note="I -> V (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 253
FT /note="I -> V (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 256
FT /note="A -> G (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 261
FT /note="I -> T (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 288
FT /note="Y -> H (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
FT CONFLICT 320
FT /note="H -> R (in Ref. 1; AAB63297)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 383 AA; 42243 MW; E2FD4C64C8C9C051 CRC64;
MDALEITQKL ISYPTITPKE CGIFEYIKSL FPHFKTLECG ENGVKNLFLY RIFNPPKDHA
EEKHAKENTK PLHFCFAGHI DVVPPGNHWQ SDPFKPVIKE GFLYGRGAQD MKGGVGAFLS
ASLNFNPKTP FLLSILLTSD EEGPGIFGTR LMLEKLKEKD LLPHMAIVAE PTCEKVLGDS
IKIGRRGSIN GKLILKGVQG HVAYPQKCQN PIDTLASVLP LISGVNLDNG DEYFDPSKLV
ITNLHAGLGA NNITPASVEI IFNARHSLKT TKESLKEYLE KVLKDLPYTL ELESSSSPFI
TASHSKLTSV LKENILKTCH TTPLLNTKGG TSDARFFSAH GIEVVEFGVI NDRIHAIDER
VSLKELELLE KVFLGVLEGL SEA
