ID   GARL_ECOLI              Reviewed;         256 AA.
AC   P23522; Q2M983;
DT   01-NOV-1991, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1995, sequence version 2.
DT   24-JAN-2024, entry version 171.
DE   RecName: Full=5-keto-4-deoxy-D-glucarate aldolase {ECO:0000303|PubMed:9772162};
DE            Short=KDGluc aldolase {ECO:0000303|PubMed:9772162};
DE            Short=KDGlucA {ECO:0000303|PubMed:9772162};
DE            EC=4.1.2.20 {ECO:0000269|PubMed:9772162, ECO:0000269|Ref.5};
DE   AltName: Full=2-dehydro-3-deoxy-D-glucarate aldolase;
DE   AltName: Full=2-keto-3-deoxy-D-glucarate aldolase {ECO:0000303|Ref.5};
DE   AltName: Full=5-dehydro-4-deoxy-D-glucarate aldolase;
DE   AltName: Full=Alpha-keto-beta-deoxy-D-glucarate aldolase;
GN   Name=garL {ECO:0000303|PubMed:10762278}; Synonyms=yhaF;
GN   OrderedLocusNames=b3126, JW3095;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
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   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 89-256.
RC   STRAIN=K12;
RX   PubMed=1705543; DOI=10.1128/jb.173.5.1813-1816.1991;
RA   Komine Y., Inokuchi H.;
RT   "Precise mapping of the rnpB gene encoding the RNA component of RNase P in
RT   Escherichia coli K-12.";
RL   J. Bacteriol. 173:1813-1816(1991).
RN   [4]
RP   PROTEIN SEQUENCE OF 1-16, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS,
RP   AND PATHWAY.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9772162; DOI=10.1021/bi981124f;
RA   Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.;
RT   "Evolution of enzymatic activities in the enolase superfamily:
RT   characterization of the (D)-glucarate/galactarate catabolic pathway in
RT   Escherichia coli.";
RL   Biochemistry 37:14369-14375(1998).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, ACTIVITY
RP   REGULATION, AND PH DEPENDENCE.
RC   STRAIN=K12 / CR63;
RA   Fish D.C., Blumenthal H.J.;
RT   "2-keto-3-deoxy-D-glucarate aldolase.";
RL   Methods Enzymol. 9:529-534(1966).
RN   [6]
RP   GENE NAME, AND INDUCTION.
RX   PubMed=10762278; DOI=10.1128/jb.182.9.2672-2674.2000;
RA   Monterrubio R., Baldoma L., Obradors N., Aguilar J., Badia J.;
RT   "A common regulator for the operons encoding the enzymes involved in D-
RT   galactarate, D-glucarate, and D-glycerate utilization in Escherichia
RT   coli.";
RL   J. Bacteriol. 182:2672-2674(2000).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND
RP   PYRUVATE, AND SUBUNIT.
RX   PubMed=10921867; DOI=10.1093/emboj/19.15.3849;
RA   Izard T., Blackwell N.C.;
RT   "Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate
RT   aldolase suggest a novel reaction mechanism.";
RL   EMBO J. 19:3849-3856(2000).
CC   -!- FUNCTION: Catalyzes the reversible retro-aldol cleavage of both 5-keto-
CC       4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and
CC       tartronic semialdehyde. {ECO:0000269|PubMed:9772162,
CC       ECO:0000269|Ref.5}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=5-dehydro-4-deoxy-D-glucarate = 2-hydroxy-3-oxopropanoate +
CC         pyruvate; Xref=Rhea:RHEA:27726, ChEBI:CHEBI:15361, ChEBI:CHEBI:42819,
CC         ChEBI:CHEBI:57978; Evidence={ECO:0000269|PubMed:9772162,
CC         ECO:0000269|Ref.5};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-dehydro-3-deoxy-D-glucarate = 2-hydroxy-3-oxopropanoate +
CC         pyruvate; Xref=Rhea:RHEA:10268, ChEBI:CHEBI:15361, ChEBI:CHEBI:57978,
CC         ChEBI:CHEBI:58098; EC=4.1.2.20; Evidence={ECO:0000269|PubMed:9772162,
CC         ECO:0000269|Ref.5};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000269|Ref.5};
CC       Name=Co(2+); Xref=ChEBI:CHEBI:48828; Evidence={ECO:0000269|Ref.5};
CC       Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000269|Ref.5};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000269|Ref.5};
CC       Note=Binds 1 Mg(2+) ion per subunit. Can also use, although less
CC       efficiently, Co(2+), Fe(2+) and Mn(2+). {ECO:0000269|Ref.5};
CC   -!- ACTIVITY REGULATION: Inhibited by acetate, chloride and bromide ions,
CC       nitrate, fluoride, cyanide, EDTA and pyrophosphate.
CC       {ECO:0000269|Ref.5}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=65 uM for 5-keto-4-deoxy-D-glucarate {ECO:0000269|PubMed:9772162};
CC       pH dependence:
CC         Optimum pH is 7.4-8.6. Stable from pH 6 to 7.5. {ECO:0000269|Ref.5};
CC   -!- PATHWAY: Carbohydrate acid metabolism; galactarate degradation; D-
CC       glycerate from galactarate: step 2/3. {ECO:0000269|PubMed:9772162}.
CC   -!- SUBUNIT: Homohexamer; trimer of dimers. {ECO:0000269|PubMed:10921867}.
CC   -!- INDUCTION: Induced by D-galactarate, D-glucarate and D-glycerate.
CC       {ECO:0000269|PubMed:10762278}.
CC   -!- MISCELLANEOUS: The catalytic mechanism was originally thought to use a
CC       phosphate as the catalytic acid, but this was subsequently disputed
CC       (PubMed:15996099, PubMed:17881002, PubMed:18754683).
CC       {ECO:0000305|PubMed:10921867}.
CC   -!- SIMILARITY: Belongs to the HpcH/HpaI aldolase family. KDGluc aldolase
CC       subfamily. {ECO:0000305}.
CC   -!- CAUTION: Was wrongly named 2-dehydro-3-deoxygalactarate aldolase (DDG
CC       aldolase or DDGA) in PubMed:10921867. 2-dehydro-3-deoxygalactarate is
CC       the enantiomer of 5-dehydro-4-deoxy-D-glucarate, but is not an isomer
CC       obtained in the degradation pathway of D-glucarate/galactarate and the
CC       enzyme has not been shown to be active on it. {ECO:0000305}.
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DR   EMBL; U18997; AAA57929.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC76160.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77173.1; -; Genomic_DNA.
DR   EMBL; D90212; BAA14237.1; -; Genomic_DNA.
DR   PIR; B65102; B65102.
DR   RefSeq; NP_417595.1; NC_000913.3.
DR   RefSeq; WP_001058209.1; NZ_LN832404.1.
DR   PDB; 1DXE; X-ray; 1.80 A; A/B=1-256.
DR   PDB; 1DXF; X-ray; 2.60 A; A/B=1-256.
DR   PDBsum; 1DXE; -.
DR   PDBsum; 1DXF; -.
DR   AlphaFoldDB; P23522; -.
DR   SMR; P23522; -.
DR   BioGRID; 4259487; 5.
DR   BioGRID; 851943; 1.
DR   DIP; DIP-9740N; -.
DR   IntAct; P23522; 9.
DR   STRING; 511145.b3126; -.
DR   jPOST; P23522; -.
DR   PaxDb; 511145-b3126; -.
DR   EnsemblBacteria; AAC76160; AAC76160; b3126.
DR   GeneID; 947630; -.
DR   KEGG; ecj:JW3095; -.
DR   KEGG; eco:b3126; -.
DR   PATRIC; fig|1411691.4.peg.3606; -.
DR   EchoBASE; EB0016; -.
DR   eggNOG; COG3836; Bacteria.
DR   HOGENOM; CLU_059964_1_0_6; -.
DR   InParanoid; P23522; -.
DR   OMA; HQVQIGC; -.
DR   OrthoDB; 86160at2; -.
DR   PhylomeDB; P23522; -.
DR   BioCyc; EcoCyc:KDGALDOL-MONOMER; -.
DR   BioCyc; MetaCyc:KDGALDOL-MONOMER; -.
DR   BRENDA; 4.1.2.20; 2026.
DR   SABIO-RK; P23522; -.
DR   UniPathway; UPA00565; UER00630.
DR   EvolutionaryTrace; P23522; -.
DR   PRO; PR:P23522; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR   GO; GO:0008672; F:2-dehydro-3-deoxyglucarate aldolase activity; IDA:EcoliWiki.
DR   GO; GO:0016832; F:aldehyde-lyase activity; IBA:GO_Central.
DR   GO; GO:0016830; F:carbon-carbon lyase activity; IDA:EcoliWiki.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0042838; P:D-glucarate catabolic process; IDA:EcoCyc.
DR   GO; GO:0046392; P:galactarate catabolic process; IDA:EcoCyc.
DR   GO; GO:0019394; P:glucarate catabolic process; IDA:EcoliWiki.
DR   Gene3D; 3.20.20.60; Phosphoenolpyruvate-binding domains; 1.
DR   HAMAP; MF_01291; KDGluc_aldolase; 1.
DR   InterPro; IPR005000; Aldolase/citrate-lyase_domain.
DR   InterPro; IPR017648; GarL.
DR   InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR   InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR   NCBIfam; TIGR03239; GarL; 1.
DR   PANTHER; PTHR30502; 2-KETO-3-DEOXY-L-RHAMNONATE ALDOLASE; 1.
DR   PANTHER; PTHR30502:SF4; 5-KETO-4-DEOXY-D-GLUCARATE ALDOLASE; 1.
DR   Pfam; PF03328; HpcH_HpaI; 1.
DR   SUPFAM; SSF51621; Phosphoenolpyruvate/pyruvate domain; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cobalt; Direct protein sequencing; Iron; Lyase; Magnesium;
KW   Manganese; Metal-binding; Reference proteome.
FT   CHAIN           1..256
FT                   /note="5-keto-4-deoxy-D-glucarate aldolase"
FT                   /id="PRO_0000207093"
FT   ACT_SITE        50
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         151
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:10921867"
FT   BINDING         153
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000269|PubMed:10921867"
FT   BINDING         178
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:10921867"
FT   BINDING         179
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000269|PubMed:10921867"
FT   BINDING         179
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:10921867"
FT   SITE            75
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250"
FT   SITE            89
FT                   /note="Increases basicity of active site His"
FT                   /evidence="ECO:0000250"
FT   HELIX           9..15
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          20..25
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           30..36
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          42..52
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           55..64
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   TURN            65..67
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          69..75
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          77..79
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           81..89
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          94..98
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           103..111
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   TURN            116..118
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          125..127
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           128..130
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   TURN            131..134
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           138..142
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          147..152
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           155..159
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           161..165
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          172..175
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           177..183
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           193..208
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          213..216
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           220..228
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   STRAND          233..238
FT                   /evidence="ECO:0007829|PDB:1DXE"
FT   HELIX           239..254
FT                   /evidence="ECO:0007829|PDB:1DXE"
SQ   SEQUENCE   256 AA;  27384 MW;  8E6345EE3F1CFCDB CRC64;
     MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH APNDISTFIP
     QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV ETKEEAELAV ASTRYPPEGI
     RGVSVSHRAN MFGTVADYFA QSNKNITILV QIESQQGVDN VDAIAATEGV DGIFVGPSDL
     AAALGHLGNA SHPDVQKAIQ HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL
     GVFRSATQKL ADTFKK
//