RHMD_SHISS
ID RHMD_SHISS Reviewed; 428 AA.
AC Q3YZV9;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 27-SEP-2005, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=L-rhamnonate dehydratase {ECO:0000255|HAMAP-Rule:MF_01288};
DE Short=RhamD {ECO:0000255|HAMAP-Rule:MF_01288};
DE EC=4.2.1.90 {ECO:0000255|HAMAP-Rule:MF_01288};
GN Name=rhmD {ECO:0000255|HAMAP-Rule:MF_01288}; OrderedLocusNames=SSON_2308;
OS Shigella sonnei (strain Ss046).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=300269;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ss046;
RX PubMed=16275786; DOI=10.1093/nar/gki954;
RA Yang F., Yang J., Zhang X., Chen L., Jiang Y., Yan Y., Tang X., Wang J.,
RA Xiong Z., Dong J., Xue Y., Zhu Y., Xu X., Sun L., Chen S., Nie H., Peng J.,
RA Xu J., Wang Y., Yuan Z., Wen Y., Yao Z., Shen Y., Qiang B., Hou Y., Yu J.,
RA Jin Q.;
RT "Genome dynamics and diversity of Shigella species, the etiologic agents of
RT bacillary dysentery.";
RL Nucleic Acids Res. 33:6445-6458(2005).
CC -!- FUNCTION: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-
CC L-rhamnonate (KDR). {ECO:0000255|HAMAP-Rule:MF_01288}.
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01288};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01288};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01288};
CC -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000255|HAMAP-
CC Rule:MF_01288}.
CC -!- MISCELLANEOUS: Reaction proceeds via a syn dehydration.
CC {ECO:0000255|HAMAP-Rule:MF_01288}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. RhamD subfamily. {ECO:0000255|HAMAP-Rule:MF_01288}.
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DR EMBL; CP000038; AAZ88953.1; -; Genomic_DNA.
DR AlphaFoldDB; Q3YZV9; -.
DR SMR; Q3YZV9; -.
DR EnsemblBacteria; AAZ88953; AAZ88953; SSON_2308.
DR KEGG; ssn:SSON_2308; -.
DR HOGENOM; CLU_030273_1_0_6; -.
DR OMA; HFVISQP; -.
DR Proteomes; UP000002529; Chromosome.
DR GO; GO:0050032; F:L-rhamnonate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
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 3: Inferred from homology;
KW Lyase; Magnesium; Metal-binding.
FT CHAIN 1..428
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351709"
FT ACT_SITE 352
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 56
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 82
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 303
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 372
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT SITE 325
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT SITE 372
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
SQ SEQUENCE 428 AA; 47895 MW; C7DCF44177421E3A CRC64;
MPAPGIFHVC WDGKVPLTYR PHNNGEHHDP TKNQTGSRLV YWRCDSRKRC WRGDYHDQGA
NHWIDDHIAT PMSKYRDYEQ SRQSFGINVL GTLIVEVEAE NGQTGFAVST AGEMGCFIVE
KHLNRFIEGK CVSDIKLIHD QMLNATLYYS GSGGLVMNTI SCVDLALWDL FGKVVGLPVY
KLLGGAVRDE IQFYATGARP DLAKEMGFIG GKMPTHWGPH DGDAGIRKDA VMVADMREKC
GEDFWLMLDC WMSQDVNYAT KLAHACAPYN LKWIEECLPP QQYEGYRELK RNAPVGMMVT
SGEHHGTLQS FRTLSETGID IMQPDVGWCG GLTTLVEIAA IAKSRGQLVV PHGSSVYSHH
AVITFTNTPF SEFLMTSPDC STMRPQFDPI LLNEPVPVNG RIHKSVLDKP GFGVELNRDC
NLKRPYSH
