RHMD_ECOLI
ID RHMD_ECOLI Reviewed; 401 AA.
AC P77215;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=L-rhamnonate dehydratase;
DE Short=RhamD;
DE EC=4.2.1.90 {ECO:0000269|PubMed:18754693};
GN Name=rhmD; Synonyms=yfaW; OrderedLocusNames=b2247, JW2241;
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 / 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 X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), FUNCTION, SUBSTRATE SPECIFICITY,
RP KINETIC PARAMETERS, SUBUNIT, CATALYTIC MECHANISM, REACTION STEREOCHEMISTRY,
RP MUTAGENESIS OF HIS-29; HIS-277 AND HIS-325, AND CATALYTIC ACTIVITY.
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).
CC -!- FUNCTION: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-
CC L-rhamnonate (KDR). Can also dehydrate L-lyxonate, L-mannonate and D-
CC gulonate, although less efficiently, but not 2-keto-4-hydroxyheptane-
CC 1,7-dioate. {ECO:0000269|PubMed:18754693}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O;
CC Xref=Rhea:RHEA:23080, ChEBI:CHEBI:15377, ChEBI:CHEBI:58118,
CC ChEBI:CHEBI:58371; EC=4.2.1.90;
CC Evidence={ECO:0000269|PubMed:18754693};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.15 mM for L-rhamnonate {ECO:0000269|PubMed:18754693};
CC KM=2.0 mM for L-lyxonate {ECO:0000269|PubMed:18754693};
CC KM=0.15 mM for L-mannonate {ECO:0000269|PubMed:18754693};
CC Note=The catalytic efficiency observed with L-rhamnonate as substrate
CC is 70- and 16-fold higher than that observed with L-lyxonate and L-
CC mannonate, respectively. {ECO:0000269|PubMed:18754693};
CC -!- SUBUNIT: Homooctamer; tetramer of dimers.
CC {ECO:0000269|PubMed:18754693}.
CC -!- MISCELLANEOUS: Reaction proceeds via a syn dehydration.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. RhamD subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA16071.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC75307.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA16071.1; ALT_INIT; Genomic_DNA.
DR PIR; E64995; E64995.
DR RefSeq; NP_416750.2; NC_000913.3.
DR RefSeq; WP_001319848.1; NZ_LN832404.1.
DR PDB; 2I5Q; X-ray; 2.10 A; A/B=1-401.
DR PDBsum; 2I5Q; -.
DR AlphaFoldDB; P77215; -.
DR SMR; P77215; -.
DR BioGRID; 4261221; 144.
DR DIP; DIP-11955N; -.
DR IntAct; P77215; 11.
DR STRING; 511145.b2247; -.
DR jPOST; P77215; -.
DR PaxDb; P77215; -.
DR PRIDE; P77215; -.
DR EnsemblBacteria; AAC75307; AAC75307; b2247.
DR EnsemblBacteria; BAA16071; BAA16071; BAA16071.
DR GeneID; 945881; -.
DR KEGG; ecj:JW2241; -.
DR KEGG; eco:b2247; -.
DR PATRIC; fig|511145.12.peg.2338; -.
DR EchoBASE; EB3838; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_1_0_6; -.
DR InParanoid; P77215; -.
DR PhylomeDB; P77215; -.
DR BioCyc; EcoCyc:G7160-MON; -.
DR BioCyc; MetaCyc:G7160-MON; -.
DR BRENDA; 4.2.1.90; 2165.
DR EvolutionaryTrace; P77215; -.
DR PRO; PR:P77215; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016836; F:hydro-lyase activity; IBA:GO_Central.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0050032; F:L-rhamnonate dehydratase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0016052; P:carbohydrate catabolic process; IBA:GO_Central.
DR GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
DR CDD; cd03327; MR_like_2; 1.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR HAMAP; MF_01288; Rhamnon_dehydrat; 1.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR023444; L-Rhamnon_dehydrat.
DR InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00006; rhamnonate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..401
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000171262"
FT ACT_SITE 325
FT /note="Proton acceptor"
FT BINDING 29
FT /ligand="substrate"
FT BINDING 55
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 222
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 345
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 298
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000250"
FT SITE 345
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT MUTAGEN 29
FT /note="H->N: Loss of L-rhamnonate dehydratase activity due
FT to absence of substrate binding."
FT /evidence="ECO:0000269|PubMed:18754693"
FT MUTAGEN 277
FT /note="H->N: 35-fold decrease in L-rhamnonate dehydratase
FT activity. 59-fold decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:18754693"
FT MUTAGEN 325
FT /note="H->N: Loss of L-rhamnonate dehydratase activity. 2-
FT fold decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:18754693"
FT STRAND 5..16
FT /evidence="ECO:0007829|PDB:2I5Q"
FT TURN 44..47
FT /evidence="ECO:0007829|PDB:2I5Q"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 65..72
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 77..83
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 85..94
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 97..100
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 108..118
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 127..148
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 160..171
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 173..178
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 182..187
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 195..213
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 215..222
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 229..239
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 256..265
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 271..274
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 281..288
FT /evidence="ECO:0007829|PDB:2I5Q"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:2I5Q"
FT TURN 299..303
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 305..317
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 329..335
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 344..347
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 350..353
FT /evidence="ECO:0007829|PDB:2I5Q"
FT TURN 359..363
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 364..366
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 374..376
FT /evidence="ECO:0007829|PDB:2I5Q"
FT HELIX 377..380
FT /evidence="ECO:0007829|PDB:2I5Q"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:2I5Q"
SQ SEQUENCE 401 AA; 44226 MW; 4622CE539229AD58 CRC64;
MTLPKIKQVR AWFTGGATAE KGAGGGDYHD QGANHWIDDH IATPMSKYRD YEQSRQSFGI
NVLGTLVVEV EAENGQTGFA VSTAGEMGCF IVEKHLNRFI EGKCVSDIKL IHDQMLSATL
YYSGSGGLVM NTISCVDLAL WDLFGKVVGL PVYKLLGGAV RDEIQFYATG ARPDLAKEMG
FIGGKMPTHW GPHDGDAGIR KDAAMVADMR EKCGEDFWLM LDCWMSQDVN YATKLAHACA
PYNLKWIEEC LPPQQYESYR ELKRNAPVGM MVTSGEHHGT LQSFRTLSET GIDIMQPDVG
WCGGLTTLVE IAAIAKSRGQ LVVPHGSSVY SHHAVITFTN TPFSEFLMTS PDCSTMRPQF
DPILLNEPVP VNGRIHKSVL DKPGFGVELN RDCNLKRPYS H
