ID   RHMD_POLSJ              Reviewed;         395 AA.
AC   Q12DF1;
DT   14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   03-AUG-2022, entry version 93.
DE   RecName: Full=L-rhamnonate dehydratase;
DE            Short=RhamD;
DE            EC=4.2.1.90;
GN   Name=rhmD; OrderedLocusNames=Bpro_1493;
OS   Polaromonas sp. (strain JS666 / ATCC BAA-500).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Polaromonas; unclassified Polaromonas.
OX   NCBI_TaxID=296591;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=JS666 / ATCC BAA-500;
RX   PubMed=18723656; DOI=10.1128/aem.00197-08;
RA   Mattes T.E., Alexander A.K., Richardson P.M., Munk A.C., Han C.S.,
RA   Stothard P., Coleman N.V.;
RT   "The genome of Polaromonas sp. strain JS666: insights into the evolution of
RT   a hydrocarbon- and xenobiotic-degrading bacterium, and features of
RT   relevance to biotechnology.";
RL   Appl. Environ. Microbiol. 74:6405-6416(2008).
RN   [2]
RP   FUNCTION AS A RHAMNONATE DEHYDRATASE.
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). {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   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC   -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000250}.
CC   -!- MISCELLANEOUS: Reaction proceeds via a syn dehydration. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC       enzyme family. RhamD subfamily. {ECO:0000305}.
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DR   EMBL; CP000316; ABE43441.1; -; Genomic_DNA.
DR   RefSeq; WP_011482440.1; NC_007948.1.
DR   AlphaFoldDB; Q12DF1; -.
DR   SMR; Q12DF1; -.
DR   STRING; 296591.Bpro_1493; -.
DR   EnsemblBacteria; ABE43441; ABE43441; Bpro_1493.
DR   KEGG; pol:Bpro_1493; -.
DR   eggNOG; COG4948; Bacteria.
DR   HOGENOM; CLU_030273_1_0_4; -.
DR   OMA; HFVISQP; -.
DR   OrthoDB; 743369at2; -.
DR   Proteomes; UP000001983; 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   1: Evidence at protein level;
KW   Lyase; Magnesium; Metal-binding; Reference proteome.
FT   CHAIN           1..395
FT                   /note="L-rhamnonate dehydratase"
FT                   /id="PRO_0000351701"
FT   ACT_SITE        319
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         23
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         49
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         215
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         241
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         269
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         339
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   SITE            292
FT                   /note="Increases basicity of active site His"
FT                   /evidence="ECO:0000250"
FT   SITE            339
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   395 AA;  44253 MW;  03B4B1791A3E5E01 CRC64;
     MNNMPTIKHV RAFTVRGGGA DYHDQGSGHW IDDHISTPMG RYPEYRQSRQ SFGINVLGTL
     VVEIEASDGT VGFSVTTGGE LGCWIVEKHL ARFIEGAKVT DIEKIWDQMF NATLYYGRKG
     IVLNTISGVD LALWDLLAKV RKEPVHALLG GPVRDELTFY ATGARPDLAK KMGFIGGKLP
     LHHGPAEREE GLKKNLELLG EMRQRVGDDF WLMYDCWMSL DVEYATRLAN AASEYKLKWI
     EEALPPDDYW GYAELRRNVP RGMLVTTGEH EATRWGFRML LEMECCDILQ PDVGWCGGIT
     ELLKISALAD AHGKLVVPHG SSVYSYHFVI TRHNSPFSEF LMMAPKADEV VPMFNPMLLD
     EPVPVNGRMK ASALDAPGFG VRLNPECALQ RPFPR