ID   RHMD_KLEP3              Reviewed;         401 AA.
AC   B5XNY1;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   25-NOV-2008, sequence version 1.
DT   03-AUG-2022, entry version 72.
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=KPK_1498;
OS   Klebsiella pneumoniae (strain 342).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX   NCBI_TaxID=507522;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=342;
RX   PubMed=18654632; DOI=10.1371/journal.pgen.1000141;
RA   Fouts D.E., Tyler H.L., DeBoy R.T., Daugherty S., Ren Q., Badger J.H.,
RA   Durkin A.S., Huot H., Shrivastava S., Kothari S., Dodson R.J., Mohamoud Y.,
RA   Khouri H., Roesch L.F.W., Krogfelt K.A., Struve C., Triplett E.W.,
RA   Methe B.A.;
RT   "Complete genome sequence of the N2-fixing broad host range endophyte
RT   Klebsiella pneumoniae 342 and virulence predictions verified in mice.";
RL   PLoS Genet. 4:E1000141-E1000141(2008).
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; CP000964; ACI08465.1; -; Genomic_DNA.
DR   AlphaFoldDB; B5XNY1; -.
DR   SMR; B5XNY1; -.
DR   EnsemblBacteria; ACI08465; ACI08465; KPK_1498.
DR   KEGG; kpe:KPK_1498; -.
DR   HOGENOM; CLU_030273_1_0_6; -.
DR   OMA; HFVISQP; -.
DR   OrthoDB; 743369at2; -.
DR   Proteomes; UP000001734; 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..401
FT                   /note="L-rhamnonate dehydratase"
FT                   /id="PRO_1000140374"
FT   ACT_SITE        325
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         29
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         55
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         222
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         248
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         276
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         345
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   SITE            298
FT                   /note="Increases basicity of active site His"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   SITE            345
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
SQ   SEQUENCE   401 AA;  44190 MW;  310BCF75B8623CF2 CRC64;
     MTLPKIKHVR AWFTGGATAE QGAGGGDYHD QGANHWIDDH IATPMSKYKE YEQSRQSFGI
     NVLGTLIVEV EADNGQTGFA VSTAGEMGCF IVEKHLNRFI EGKCVSDIKL IHDQMLNATL
     YYAGSGGLVM NTLSCVDLAL WDLFGKVVGL PVYKLLGGAV RDEIQFYATG ARPDLAQEMG
     FIGGKMPTHW GPHDGDAGIR KDVAMVADMR EKCGPDFWLM LDCWMSQDVN YATKLAHACA
     PYNLKWIEEC LPPQQYEGYR ELKRQAPAGM MVTSGEHHGT LQSFRTLSET GIDIMQPDVG
     WCGGLTTLVE IAAIAKARGQ LVVPHGSSVY SHHAVITFTN TPFSEFLMTS PDCATLRPQF
     DPILLGEPVP ERGRIHKSVL DKPGFGVELN RDCNLKRPYQ H