DAPE_NEIMB
ID DAPE_NEIMB Reviewed; 381 AA.
AC Q9JYL2;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase;
DE Short=SDAP desuccinylase;
DE EC=3.5.1.18;
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase;
GN Name=dapE; OrderedLocusNames=NMB1530;
OS Neisseria meningitidis serogroup B (strain MC58).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=122586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MC58;
RX PubMed=10710307; DOI=10.1126/science.287.5459.1809;
RA Tettelin H., Saunders N.J., Heidelberg J.F., Jeffries A.C., Nelson K.E.,
RA Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C.,
RA Gwinn M.L., DeBoy R.T., Peterson J.D., Hickey E.K., Haft D.H.,
RA Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T.M.,
RA Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D.,
RA Utterback T.R., Khouri H.M., Qin H., Vamathevan J.J., Gill J., Scarlato V.,
RA Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M.,
RA Moxon E.R., Rappuoli R., Venter J.C.;
RT "Complete genome sequence of Neisseria meningitidis serogroup B strain
RT MC58.";
RL Science 287:1809-1815(2000).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), AND SUBUNIT.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
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:0000250}.
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: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.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16021622}.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE002098; AAF41885.1; -; Genomic_DNA.
DR PIR; F81073; F81073.
DR RefSeq; NP_274537.1; NC_003112.2.
DR RefSeq; WP_002225058.1; NC_003112.2.
DR PDB; 1VGY; X-ray; 1.90 A; A/B=2-381.
DR PDB; 4O23; X-ray; 2.09 A; A/B=1-381.
DR PDB; 4PPZ; X-ray; 2.00 A; A=1-381.
DR PDB; 4PQA; X-ray; 1.78 A; A=1-381.
DR PDB; 5UEJ; X-ray; 1.30 A; A/B=1-381.
DR PDBsum; 1VGY; -.
DR PDBsum; 4O23; -.
DR PDBsum; 4PPZ; -.
DR PDBsum; 4PQA; -.
DR PDBsum; 5UEJ; -.
DR AlphaFoldDB; Q9JYL2; -.
DR SMR; Q9JYL2; -.
DR STRING; 122586.NMB1530; -.
DR PaxDb; Q9JYL2; -.
DR DNASU; 904046; -.
DR EnsemblBacteria; AAF41885; AAF41885; NMB1530.
DR KEGG; nme:NMB1530; -.
DR PATRIC; fig|122586.8.peg.1942; -.
DR HOGENOM; CLU_021802_4_0_4; -.
DR OMA; LNSHHDT; -.
DR BRENDA; 3.5.1.18; 3593.
DR UniPathway; UPA00034; UER00021.
DR EvolutionaryTrace; Q9JYL2; -.
DR Proteomes; UP000000425; 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; 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.
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..381
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375624"
FT ACT_SITE 70
FT /evidence="ECO:0000250"
FT ACT_SITE 135
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 136
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 350
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT HELIX 5..14
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 26..35
FT /evidence="ECO:0007829|PDB:5UEJ"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 40..43
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:5UEJ"
FT TURN 97..102
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 103..119
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 124..133
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:4PPZ"
FT HELIX 143..152
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 173..179
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 181..190
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 205..218
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 232..240
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 250..260
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 266..279
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 284..292
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 301..314
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 319..321
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 329..332
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 333..335
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 336..341
FT /evidence="ECO:0007829|PDB:5UEJ"
FT TURN 347..350
FT /evidence="ECO:0007829|PDB:5UEJ"
FT STRAND 355..357
FT /evidence="ECO:0007829|PDB:5UEJ"
FT HELIX 360..376
FT /evidence="ECO:0007829|PDB:5UEJ"
SQ SEQUENCE 381 AA; 41325 MW; EA64C393977C48E7 CRC64;
MTETQSLELA KELISRPSVT PDDRDCQKLL AERLHKIGFA AEELHFGDTK NIWLRRGTKA
PVVCFAGHTD VVPTGPVEKW DSPPFEPAER DGRLYGRGAA DMKTSIACFV TACERFVAKH
PNHQGSIALL ITSDEEGDAL DGTTKVVDVL KARDELIDYC IVGEPTAVDK LGDMIKNGRR
GSLSGNLTVK GKQGHIAYPH LAINPVHTFA PALLELTQEV WDEGNEYFPP TSFQISNING
GTGATNVIPG ELNVKFNFRF STESTEAGLK QRVHAILDKH GVQYDLQWSC SGQPFLTQAG
KLTDVARAAI AETCGIEAEL STTGGTSDGR FIKAIAQELI ELGPSNATIH QINENVRLND
IPKLSAVYEG ILARLLAGNA V
