GABD_ECOLI
ID GABD_ECOLI Reviewed; 482 AA.
AC P25526; P78207; P78208; P78209;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Succinate-semialdehyde dehydrogenase [NADP(+)] GabD;
DE Short=SSDH;
DE EC=1.2.1.79;
DE AltName: Full=Glutarate-semialdehyde dehydrogenase {ECO:0000305|PubMed:30498244};
DE EC=1.2.1.- {ECO:0000269|PubMed:30498244};
GN Name=gabD; OrderedLocusNames=b2661, JW2636;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / JM103 / ATCC 39403 / DSM 2829 / KCTC 1112 / NCIMB 12044;
RX PubMed=8297211; DOI=10.1007/bf00245306;
RA Niegemann E., Schulz A., Bartsch K.;
RT "Molecular organization of the Escherichia coli gab cluster: nucleotide
RT sequence of the structural genes gabD and gabP and expression of the GABA
RT permease gene.";
RL Arch. Microbiol. 160:454-460(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, AND INDUCTION.
RC STRAIN=K12;
RX PubMed=7011797; DOI=10.1111/j.1432-1033.1981.tb05098.x;
RA Donnelly M.I., Cooper R.A.;
RT "Succinic semialdehyde dehydrogenases of Escherichia coli: their role in
RT the degradation of p-hydroxyphenylacetate and gamma-aminobutyrate.";
RL Eur. J. Biochem. 113:555-561(1981).
RN [6]
RP INDUCTION.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=14731280; DOI=10.1046/j.1365-2958.2003.03867.x;
RA Metzner M., Germer J., Hengge R.;
RT "Multiple stress signal integration in the regulation of the complex sigma
RT S-dependent csiD-ygaF-gabDTP operon in Escherichia coli.";
RL Mol. Microbiol. 51:799-811(2004).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=K12 / BW25113;
RX PubMed=30498244; DOI=10.1038/s41467-018-07563-6;
RA Knorr S., Sinn M., Galetskiy D., Williams R.M., Wang C., Mueller N.,
RA Mayans O., Schleheck D., Hartig J.S.;
RT "Widespread bacterial lysine degradation proceeding via glutarate and L-2-
RT hydroxyglutarate.";
RL Nat. Commun. 9:5071-5071(2018).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NADP(+), FUNCTION,
RP CATALYTIC ACTIVITY, KINETIC PARAMETERS, REACTION MECHANISM, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=20174634; DOI=10.1371/journal.pone.0009280;
RA Langendorf C.G., Key T.L., Fenalti G., Kan W.T., Buckle A.M.,
RA Caradoc-Davies T., Tuck K.L., Law R.H., Whisstock J.C.;
RT "The X-ray crystal structure of Escherichia coli succinic semialdehyde
RT dehydrogenase; structural insights into NADP+/enzyme interactions.";
RL PLoS ONE 5:E9280-E9280(2010).
CC -!- FUNCTION: Catalyzes the NADP(+)-dependent oxidation of succinate
CC semialdehyde to succinate (PubMed:20174634). Thereby functions in a
CC GABA degradation pathway that allows some E.coli strains to utilize
CC GABA as a nitrogen source for growth (PubMed:7011797). Also catalyzes
CC the conversion of glutarate semialdehyde to glutarate, as part of a L-
CC lysine degradation pathway that proceeds via cadaverine, glutarate and
CC L-2-hydroxyglutarate (PubMed:30498244). {ECO:0000269|PubMed:20174634,
CC ECO:0000269|PubMed:30498244, ECO:0000305|PubMed:7011797}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NADP(+) + succinate semialdehyde = 2 H(+) + NADPH +
CC succinate; Xref=Rhea:RHEA:13213, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30031, ChEBI:CHEBI:57706,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.2.1.79;
CC Evidence={ECO:0000269|PubMed:20174634};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13214;
CC Evidence={ECO:0000305|PubMed:20174634};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-oxopentanoate + H2O + NADP(+) = glutarate + 2 H(+) + NADPH;
CC Xref=Rhea:RHEA:57832, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16120, ChEBI:CHEBI:30921, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349; Evidence={ECO:0000269|PubMed:30498244};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:57833;
CC Evidence={ECO:0000305|PubMed:30498244};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=16.94 uM for succinate semialdehyde {ECO:0000269|PubMed:20174634};
CC Note=The succinate-semialdehyde dehydrogenase activity measured in
CC the presence of NADP(+) is approximately 20-fold higher than that
CC measured in the presence of NAD(+).;
CC -!- PATHWAY: Amino-acid degradation; 4-aminobutanoate degradation.
CC {ECO:0000305|PubMed:7011797}.
CC -!- PATHWAY: Amino-acid degradation. {ECO:0000305|PubMed:30498244}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:20174634}.
CC -!- INDUCTION: Induced by RpoS in response to multiple stress conditions,
CC including shifts to acidic pH, nitrogen limitation or high osmolarity
CC as well as starvation or stationary phase (PubMed:14731280). Induced by
CC gamma-aminobutyrate (GABA) (PubMed:7011797).
CC {ECO:0000269|PubMed:14731280, ECO:0000269|PubMed:7011797}.
CC -!- SIMILARITY: Belongs to the aldehyde dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; M88334; AAC36831.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75708.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16524.2; -; Genomic_DNA.
DR PIR; F65045; F65045.
DR RefSeq; NP_417147.1; NC_000913.3.
DR RefSeq; WP_000772831.1; NZ_LN832404.1.
DR PDB; 3JZ4; X-ray; 2.30 A; A/B/C/D=2-482.
DR PDBsum; 3JZ4; -.
DR AlphaFoldDB; P25526; -.
DR SMR; P25526; -.
DR BioGRID; 4259209; 53.
DR DIP; DIP-9723N; -.
DR IntAct; P25526; 3.
DR STRING; 511145.b2661; -.
DR jPOST; P25526; -.
DR PaxDb; P25526; -.
DR PRIDE; P25526; -.
DR EnsemblBacteria; AAC75708; AAC75708; b2661.
DR EnsemblBacteria; BAA16524; BAA16524; BAA16524.
DR GeneID; 948060; -.
DR KEGG; ecj:JW2636; -.
DR KEGG; eco:b2661; -.
DR PATRIC; fig|1411691.4.peg.4080; -.
DR EchoBASE; EB1305; -.
DR eggNOG; COG1012; Bacteria.
DR HOGENOM; CLU_005391_5_1_6; -.
DR InParanoid; P25526; -.
DR OMA; WHRLILE; -.
DR PhylomeDB; P25526; -.
DR BioCyc; EcoCyc:SUCCSEMIALDDEHYDROG-MON; -.
DR BioCyc; MetaCyc:SUCCSEMIALDDEHYDROG-MON; -.
DR BRENDA; 1.2.1.79; 2026.
DR UniPathway; UPA00733; -.
DR PRO; PR:P25526; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0102810; F:glutarate-semialdehyde dehydrogenase (NADP+) activity; IDA:EcoCyc.
DR GO; GO:0050661; F:NADP binding; IDA:UniProtKB.
DR GO; GO:0004777; F:succinate-semialdehyde dehydrogenase (NAD+) activity; IDA:UniProtKB.
DR GO; GO:0036243; F:succinate-semialdehyde dehydrogenase (NADP+) activity; IDA:EcoCyc.
DR GO; GO:0009013; F:succinate-semialdehyde dehydrogenase [NAD(P)+] activity; IDA:UniProtKB.
DR GO; GO:0009450; P:gamma-aminobutyric acid catabolic process; IDA:UniProtKB.
DR GO; GO:0006807; P:nitrogen compound metabolic process; IDA:UniProtKB.
DR Gene3D; 3.40.309.10; -; 1.
DR Gene3D; 3.40.605.10; -; 1.
DR InterPro; IPR016161; Ald_DH/histidinol_DH.
DR InterPro; IPR016163; Ald_DH_C.
DR InterPro; IPR016160; Ald_DH_CS_CYS.
DR InterPro; IPR029510; Ald_DH_CS_GLU.
DR InterPro; IPR016162; Ald_DH_N.
DR InterPro; IPR015590; Aldehyde_DH_dom.
DR InterPro; IPR010102; Succ_semiAld_DH.
DR Pfam; PF00171; Aldedh; 1.
DR SUPFAM; SSF53720; SSF53720; 1.
DR TIGRFAMs; TIGR01780; SSADH; 1.
DR PROSITE; PS00070; ALDEHYDE_DEHYDR_CYS; 1.
DR PROSITE; PS00687; ALDEHYDE_DEHYDR_GLU; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..482
FT /note="Succinate-semialdehyde dehydrogenase [NADP(+)] GabD"
FT /id="PRO_0000056572"
FT ACT_SITE 255
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:20174634"
FT ACT_SITE 289
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:20174634"
FT BINDING 156..157
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:20174634"
FT BINDING 180..183
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:20174634"
FT BINDING 233..234
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:20174634"
FT BINDING 256
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:20174634"
FT BINDING 386
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:20174634"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 12..15
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:3JZ4"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 47..66
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 69..85
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 87..98
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 102..122
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 128..131
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 138..146
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 161..173
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 187..199
FT /evidence="ECO:0007829|PDB:3JZ4"
FT TURN 203..205
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 214..222
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 226..233
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 235..245
FT /evidence="ECO:0007829|PDB:3JZ4"
FT TURN 246..249
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 251..255
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 270..282
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 283..286
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 291..298
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 302..313
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 334..349
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 353..356
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 371..375
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 381..383
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 389..397
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 400..408
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 414..419
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 423..432
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 436..441
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 448..450
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 456..458
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 459..461
FT /evidence="ECO:0007829|PDB:3JZ4"
FT HELIX 465..470
FT /evidence="ECO:0007829|PDB:3JZ4"
FT STRAND 473..481
FT /evidence="ECO:0007829|PDB:3JZ4"
SQ SEQUENCE 482 AA; 51720 MW; 091538F8741DB0CF CRC64;
MKLNDSNLFR QQALINGEWL DANNGEAIDV TNPANGDKLG SVPKMGADET RAAIDAANRA
LPAWRALTAK ERATILRNWF NLMMEHQDDL ARLMTLEQGK PLAEAKGEIS YAASFIEWFA
EEGKRIYGDT IPGHQADKRL IVIKQPIGVT AAITPWNFPA AMITRKAGPA LAAGCTMVLK
PASQTPFSAL ALAELAIRAG VPAGVFNVVT GSAGAVGNEL TSNPLVRKLS FTGSTEIGRQ
LMEQCAKDIK KVSLELGGNA PFIVFDDADL DKAVEGALAS KFRNAGQTCV CANRLYVQDG
VYDRFAEKLQ QAVSKLHIGD GLDNGVTIGP LIDEKAVAKV EEHIADALEK GARVVCGGKA
HERGGNFFQP TILVDVPANA KVSKEETFGP LAPLFRFKDE ADVIAQANDT EFGLAAYFYA
RDLSRVFRVG EALEYGIVGI NTGIISNEVA PFGGIKASGL GREGSKYGIE DYLEIKYMCI
GL
