DGOA_ECOLI
ID DGOA_ECOLI Reviewed; 205 AA.
AC Q6BF16; P31458; Q2M805;
DT 23-NOV-2004, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=2-dehydro-3-deoxy-6-phosphogalactonate aldolase;
DE EC=4.1.2.21;
DE AltName: Full=2-oxo-3-deoxygalactonate 6-phosphate aldolase;
DE AltName: Full=6-phospho-2-dehydro-3-deoxygalactonate aldolase;
DE AltName: Full=6-phospho-2-keto-3-deoxygalactonate aldolase;
DE Short=KDPGal;
GN Name=dgoA; Synonyms=yidU; OrderedLocusNames=b4477, JW5628;
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=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [2]
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 [3]
RP SEQUENCE REVISION.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
RN [4]
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 [5]
RP FUNCTION, AND INDUCTION.
RX PubMed=324806; DOI=10.1016/0014-5793(77)80234-2;
RA Deacon J., Cooper R.A.;
RT "D-galactonate utilisation by enteric bacteria. The catabolic pathway in
RT Escherichia coli.";
RL FEBS Lett. 77:201-205(1977).
RN [6]
RP INDUCTION, OPERON, AND DISRUPTION PHENOTYPE.
RX PubMed=30455279; DOI=10.1128/jb.00281-18;
RA Singh B., Arya G., Kundu N., Sangwan A., Nongthombam S., Chaba R.;
RT "Molecular and functional insights into the regulation of D-galactonate
RT metabolism by the transcriptional regulator DgoR in Escherichia coli.";
RL J. Bacteriol. 201:e00281-e00281(2019).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, FUNCTION,
RP CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-37 AND VAL-154, ACTIVE SITE,
RP BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY, SUBSTRATE SPECIFICITY,
RP AND SUBUNIT.
RX PubMed=17981470; DOI=10.1016/j.bmc.2007.10.043;
RA Walters M.J., Srikannathasan V., McEwan A.R., Naismith J.H., Fierke C.A.,
RA Toone E.J.;
RT "Characterization and crystal structure of Escherichia coli KDPGal
RT aldolase.";
RL Bioorg. Med. Chem. 16:710-720(2008).
CC -!- FUNCTION: Involved in the degradation of galactose via the DeLey-
CC Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol
CC cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate
CC and D-glyceraldehyde-3-phosphate. In the synthetic direction, it
CC catalyzes the addition of pyruvate to electrophilic aldehydes with re-
CC facial selectivity. It can use a limited number of aldehyde substrates,
CC including D-glyceraldehyde-3-phosphate (natural substrate), D-
CC glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-
CC erythrose and D-threose. It efficiently catalyzes aldol addition only
CC using pyruvate as the nucleophilic component and accepts both
CC stereochemical configurations at C2 of the electrophile.
CC {ECO:0000269|PubMed:17981470, ECO:0000269|PubMed:324806}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-dehydro-3-deoxy-6-phospho-D-galactonate = D-glyceraldehyde
CC 3-phosphate + pyruvate; Xref=Rhea:RHEA:24464, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:58298, ChEBI:CHEBI:59776; EC=4.1.2.21;
CC Evidence={ECO:0000269|PubMed:17981470};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.2 mM for KDPGal {ECO:0000269|PubMed:17981470};
CC Note=kcat is 4 sec(-1) for KDPGal.;
CC -!- PATHWAY: Carbohydrate acid metabolism; D-galactonate degradation; D-
CC glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 3/3.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:17981470}.
CC -!- INDUCTION: Part of the dgoRKADT operon, which encodes proteins for the
CC metabolism of D-galactonate (PubMed:30455279). Negatively regulated by
CC DgoR (PubMed:30455279). Expression is induced in the presence of D-
CC galactonate and galactose (PubMed:30455279, PubMed:324806).
CC {ECO:0000269|PubMed:30455279, ECO:0000269|PubMed:324806}.
CC -!- MASS SPECTROMETRY: Mass=21383; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:17981470};
CC -!- DISRUPTION PHENOTYPE: Deletion mutant cannot grow on D-galactonate.
CC {ECO:0000269|PubMed:30455279}.
CC -!- SIMILARITY: Belongs to the KHG/KDPG aldolase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA62044.1; Type=Frameshift; Note=The frameshift in position 204 caused the prediction of an ORF that fused dgoA and dgoD.; Evidence={ECO:0000305};
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DR EMBL; L10328; AAA62044.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00096; AAT48198.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77601.1; -; Genomic_DNA.
DR PIR; E65171; E65171.
DR RefSeq; WP_001198722.1; NZ_SSZK01000035.1.
DR RefSeq; YP_026238.1; NC_000913.3.
DR PDB; 2V81; X-ray; 2.40 A; A=1-205.
DR PDB; 2V82; X-ray; 2.10 A; A=1-205.
DR PDB; 4QCC; X-ray; 7.08 A; A/B=1-203.
DR PDBsum; 2V81; -.
DR PDBsum; 2V82; -.
DR PDBsum; 4QCC; -.
DR AlphaFoldDB; Q6BF16; -.
DR SMR; Q6BF16; -.
DR BioGRID; 4260839; 13.
DR STRING; 511145.b4477; -.
DR ChEMBL; CHEMBL4296324; -.
DR PaxDb; Q6BF16; -.
DR PRIDE; Q6BF16; -.
DR EnsemblBacteria; AAT48198; AAT48198; b4477.
DR EnsemblBacteria; BAE77601; BAE77601; BAE77601.
DR GeneID; 2847766; -.
DR KEGG; ecj:JW5628; -.
DR KEGG; eco:b4477; -.
DR PATRIC; fig|1411691.4.peg.3010; -.
DR EchoBASE; EB1667; -.
DR eggNOG; COG0800; Bacteria.
DR HOGENOM; CLU_077795_2_1_6; -.
DR InParanoid; Q6BF16; -.
DR OMA; HGPIPEV; -.
DR PhylomeDB; Q6BF16; -.
DR BioCyc; EcoCyc:DEHYDDEOXPHOSGALACT-ALDOL-MON; -.
DR BioCyc; MetaCyc:DEHYDDEOXPHOSGALACT-ALDOL-MON; -.
DR BRENDA; 4.1.2.21; 2026.
DR UniPathway; UPA00081; UER00520.
DR EvolutionaryTrace; Q6BF16; -.
DR PRO; PR:Q6BF16; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008674; F:2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity; IDA:EcoCyc.
DR GO; GO:0034194; P:D-galactonate catabolic process; IMP:EcoCyc.
DR CDD; cd00452; KDPG_aldolase; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR000887; Aldlse_KDPG_KHG.
DR InterPro; IPR013785; Aldolase_TIM.
DR PANTHER; PTHR30246; PTHR30246; 1.
DR Pfam; PF01081; Aldolase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Reference proteome.
FT CHAIN 1..205
FT /note="2-dehydro-3-deoxy-6-phosphogalactonate aldolase"
FT /id="PRO_0000079880"
FT ACT_SITE 37
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17981470"
FT ACT_SITE 126
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000269|PubMed:17981470"
FT BINDING 14
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17981470"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17981470"
FT BINDING 126
FT /ligand="substrate"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17981470"
FT BINDING 156
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 176..177
FT /ligand="substrate"
FT SITE 14
FT /note="Orients the nucleophilic substrate"
FT SITE 154
FT /note="Plays a major role in determining the
FT stereoselectivity"
FT MUTAGEN 37
FT /note="E->N: 50-fold decrease in catalytic efficiency and
FT 6-fold decrease of binding affinity."
FT /evidence="ECO:0000269|PubMed:17981470"
FT MUTAGEN 154
FT /note="V->T: Little stereoselectivity, accepting KDPG and
FT KDPGal as substrate with roughly equal efficacy. Reduced
FT the preference for KDPGal. It diminishes the activity
FT against KDPGal and increases activity against KDPG."
FT /evidence="ECO:0000269|PubMed:17981470"
FT STRAND 5..7
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 9..12
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 18..31
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 35..39
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 45..56
FT /evidence="ECO:0007829|PDB:2V82"
FT TURN 57..59
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 91..99
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:2V81"
FT HELIX 111..119
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 130..133
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 135..142
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:2V82"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 162..168
FT /evidence="ECO:0007829|PDB:2V82"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:2V82"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:2V82"
FT HELIX 186..205
FT /evidence="ECO:0007829|PDB:2V82"
SQ SEQUENCE 205 AA; 21391 MW; FC59B92BAAA41CE4 CRC64;
MQWQTKLPLI AILRGITPDE ALAHVGAVID AGFDAVEIPL NSPQWEQSIP AIVDAYGDKA
LIGAGTVLKP EQVDALARMG CQLIVTPNIH SEVIRRAVGY GMTVCPGCAT ATEAFTALEA
GAQALKIFPS SAFGPQYIKA LKAVLPSDIA VFAVGGVTPE NLAQWIDAGC AGAGLGSDLY
RAGQSVERTA QQAAAFVKAY REAVQ
