ID RHMA_ECOLI Reviewed; 267 AA.
AC P76469; P76925; P76926; P76928; P76929;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 24-JAN-2024, entry version 147.
DE RecName: Full=2-keto-3-deoxy-L-rhamnonate aldolase;
DE Short=KDR aldolase;
DE EC=4.1.2.53 {ECO:0000269|PubMed:18754683};
DE AltName: Full=2-dehydro-3-deoxyrhamnonate aldolase;
DE AltName: Full=2-keto-3-deoxy acid sugar aldolase;
GN Name=rhmA; Synonyms=yfaU; OrderedLocusNames=b2245, JW2239;
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 / 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 [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 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 [4]
RP CRYSTALLIZATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=12454498; DOI=10.1107/s0907444902017894;
RA Wright A., Blewett A., Fueloep V., Cooper R., Burrows S., Jones C.,
RA Roper D.;
RT "Expression, purification, crystallization and preliminary characterization
RT of an HHED aldolase homologue from Escherichia coli K12.";
RL Acta Crystallogr. D 58:2191-2193(2002).
RN [5]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=18754693; DOI=10.1021/bi800914r;
RA Rakus J.F., Fedorov A.A., Fedorov E.V., Glasner M.E., Hubbard B.K.,
RA Delli J.D., Babbitt P.C., Almo S.C., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate
RT dehydratase.";
RL Biochemistry 47:9944-9954(2008).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.39 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP MAGNESIUM AND PYRUVATE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, CATALYTIC MECHANISM, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, AND MUTAGENESIS OF HIS-49 AND ARG-74.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=18754683; DOI=10.1021/bi800943g;
RA Rea D., Hovington R., Rakus J.F., Gerlt J.A., Fueloep V., Bugg T.D.H.,
RA Roper D.I.;
RT "Crystal structure and functional assignment of YfaU, a metal ion dependent
RT class II aldolase from Escherichia coli K12.";
RL Biochemistry 47:9955-9965(2008).
CC -!- FUNCTION: Catalyzes the reversible retro-aldol cleavage of 2-keto-3-
CC deoxy-L-rhamnonate (KDR) to pyruvate and lactaldehyde. 2-keto-3-deoxy-
CC L-mannonate, 2-keto-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-
CC dioate (HKHD) are also reasonably good substrates, although 2-keto-3-
CC deoxy-L-rhamnonate is likely to be the physiological substrate.
CC {ECO:0000269|PubMed:18754683, ECO:0000269|PubMed:18754693}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-dehydro-3-deoxy-L-rhamnonate = (S)-lactaldehyde + pyruvate;
CC Xref=Rhea:RHEA:25784, ChEBI:CHEBI:15361, ChEBI:CHEBI:18041,
CC ChEBI:CHEBI:58371; EC=4.1.2.53;
CC Evidence={ECO:0000269|PubMed:18754683};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:18754683};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:18754683};
CC Note=Binds 1 Mg(2+) ion per subunit. Is more efficient when using
CC Ni(2+) ion, although it is not likely to be the physiologically
CC relevant active site metal. {ECO:0000269|PubMed:18754683};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.078 mM for 2-keto-3-deoxy-L-rhamnonate (in the presence of
CC magnesium) {ECO:0000269|PubMed:18754683};
CC KM=0.14 mM for 2-keto-3-deoxy-L-mannonate (in the presence of
CC magnesium) {ECO:0000269|PubMed:18754683};
CC KM=0.8 mM for 2-keto-3-deoxy-L-lyxonate (in the presence of
CC magnesium) {ECO:0000269|PubMed:18754683};
CC KM=0.15 mM for 4-hydroxy-2-ketoheptane-1,7-dioate (in the presence of
CC magnesium) {ECO:0000269|PubMed:18754683};
CC KM=0.1 mM for 4-hydroxy-2-ketoheptane-1,7-dioate (in the presence of
CC nickel) {ECO:0000269|PubMed:18754683};
CC KM=0.1 mM for 4-hydroxy-2-ketopentanoate (in the presence of nickel)
CC {ECO:0000269|PubMed:18754683};
CC KM=0.05 mM for 4-hydroxy-2-ketohexanoate (in the presence of nickel)
CC {ECO:0000269|PubMed:18754683};
CC Note=The catalytic efficiency observed with HKHD as substrate is 750-
CC fold higher with Ni(2+) as cofactor than that with Mg(2+) as
CC cofactor. 4-hydroxy-2-keto-5-phenyl-pentanoate and 4-hydroxy-2-keto-
CC 6-phenylhexanoate are not substrates, suggesting a requirement for an
CC aliphatic or less bulky distal end of the substrate.;
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:18754683}.
CC -!- SIMILARITY: Belongs to the HpcH/HpaI aldolase family. KDR aldolase
CC subfamily. {ECO:0000305}.
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DR EMBL; U00096; AAC75305.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16064.2; -; Genomic_DNA.
DR PIR; C64995; C64995.
DR RefSeq; NP_416748.1; NC_000913.3.
DR RefSeq; WP_000992954.1; NZ_LN832404.1.
DR PDB; 2VWS; X-ray; 1.39 A; A/B/C=1-267.
DR PDB; 2VWT; X-ray; 1.93 A; A/B/C=1-267.
DR PDBsum; 2VWS; -.
DR PDBsum; 2VWT; -.
DR AlphaFoldDB; P76469; -.
DR SMR; P76469; -.
DR BioGRID; 4261484; 18.
DR DIP; DIP-11953N; -.
DR STRING; 511145.b2245; -.
DR PaxDb; 511145-b2245; -.
DR EnsemblBacteria; AAC75305; AAC75305; b2245.
DR GeneID; 948054; -.
DR KEGG; ecj:JW2239; -.
DR KEGG; eco:b2245; -.
DR PATRIC; fig|511145.12.peg.2336; -.
DR EchoBASE; EB3836; -.
DR eggNOG; COG3836; Bacteria.
DR HOGENOM; CLU_059964_1_0_6; -.
DR InParanoid; P76469; -.
DR OMA; YVDLEHT; -.
DR OrthoDB; 86160at2; -.
DR PhylomeDB; P76469; -.
DR BioCyc; EcoCyc:G7158-MONOMER; -.
DR BioCyc; MetaCyc:G7158-MONOMER; -.
DR BRENDA; 4.1.2.53; 2026.
DR EvolutionaryTrace; P76469; -.
DR PRO; PR:P76469; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0106099; F:2-keto-3-deoxy-L-rhamnonate aldolase activity; IDA:EcoCyc.
DR GO; GO:0016832; F:aldehyde-lyase activity; IDA:EcoliWiki.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016151; F:nickel cation binding; IDA:EcoliWiki.
DR GO; GO:0034214; P:protein hexamerization; IDA:EcoCyc.
DR Gene3D; 3.20.20.60; Phosphoenolpyruvate-binding domains; 1.
DR HAMAP; MF_01290; KDR_aldolase; 1.
DR InterPro; IPR005000; Aldolase/citrate-lyase_domain.
DR InterPro; IPR023593; KDR_aldolase.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR PANTHER; PTHR30502; 2-KETO-3-DEOXY-L-RHAMNONATE ALDOLASE; 1.
DR PANTHER; PTHR30502:SF5; 2-KETO-3-DEOXY-L-RHAMNONATE ALDOLASE; 1.
DR Pfam; PF03328; HpcH_HpaI; 1.
DR SUPFAM; SSF51621; Phosphoenolpyruvate/pyruvate domain; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Nickel; Reference proteome.
FT CHAIN 1..267
FT /note="2-keto-3-deoxy-L-rhamnonate aldolase"
FT /id="PRO_0000207094"
FT ACT_SITE 49
FT /note="Proton acceptor"
FT BINDING 151
FT /ligand="substrate"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18754683"
FT BINDING 178
FT /ligand="substrate"
FT BINDING 179
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:18754683"
FT BINDING 179
FT /ligand="substrate"
FT SITE 74
FT /note="Transition state stabilizer"
FT SITE 88
FT /note="Increases basicity of active site His"
FT MUTAGEN 49
FT /note="H->A: Loss of 2-keto-3-deoxy-L-rhamnonate aldolase
FT activity."
FT /evidence="ECO:0000269|PubMed:18754683"
FT MUTAGEN 74
FT /note="R->A: Loss of 2-keto-3-deoxy-L-rhamnonate aldolase
FT activity."
FT /evidence="ECO:0000269|PubMed:18754683"
FT HELIX 8..14
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 19..24
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 29..36
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 41..46
FT /evidence="ECO:0007829|PDB:2VWS"
FT TURN 47..49
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 54..64
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 67..74
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 80..88
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 102..111
FT /evidence="ECO:0007829|PDB:2VWS"
FT TURN 115..117
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 128..133
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 138..145
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 155..159
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 161..165
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 177..183
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 193..208
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 212..216
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 220..228
FT /evidence="ECO:0007829|PDB:2VWS"
FT STRAND 233..238
FT /evidence="ECO:0007829|PDB:2VWS"
FT HELIX 239..252
FT /evidence="ECO:0007829|PDB:2VWS"
SQ SEQUENCE 267 AA; 28916 MW; F68506D8A11D23FE CRC64;
MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA PNTIQDLYHQ
LQAVAPYASQ PVIRPVEGSK PLIKQVLDIG AQTLLIPMVD TAEQARQVVS ATRYPPYGER
GVGASVARAA RWGRIENYMA QVNDSLCLLV QVESKTALDN LDEILDVEGI DGVFIGPADL
SASLGYPDNA GHPEVQRIIE TSIRRIRAAG KAAGFLAVAP DMAQQCLAWG ANFVAVGVDT
MLYSDALDQR LAMFKSGKNG PRIKGSY
//
