GARL_ECOLI
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 03-AUG-2022, entry version 165.
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; Proteobacteria; 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 and 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; P23522; -.
DR PRIDE; P23522; -.
DR EnsemblBacteria; AAC76160; AAC76160; b3126.
DR EnsemblBacteria; BAE77173; BAE77173; BAE77173.
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; NEGWMVK; -.
DR PhylomeDB; P23522; -.
DR BioCyc; EcoCyc:KDGALDOL-MON; -.
DR BioCyc; MetaCyc:KDGALDOL-MON; -.
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; -; 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 Pfam; PF03328; HpcH_HpaI; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
DR TIGRFAMs; TIGR03239; GarL; 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
