ID   RHMD_PARPJ              Reviewed;         392 AA.
AC   B2TFM7;
DT   14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-2008, sequence version 1.
DT   03-AUG-2022, entry version 78.
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=Bphyt_5689;
OS   Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)
OS   (Burkholderia phytofirmans).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=398527;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 17436 / LMG 22146 / PsJN;
RX   PubMed=21551308; DOI=10.1128/jb.05055-11;
RA   Weilharter A., Mitter B., Shin M.V., Chain P.S., Nowak J., Sessitsch A.;
RT   "Complete genome sequence of the plant growth-promoting endophyte
RT   Burkholderia phytofirmans strain PsJN.";
RL   J. Bacteriol. 193:3383-3384(2011).
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; CP001053; ACD20035.1; -; Genomic_DNA.
DR   RefSeq; WP_012427543.1; NC_010676.1.
DR   AlphaFoldDB; B2TFM7; -.
DR   SMR; B2TFM7; -.
DR   STRING; 398527.Bphyt_5689; -.
DR   EnsemblBacteria; ACD20035; ACD20035; Bphyt_5689.
DR   KEGG; bpy:Bphyt_5689; -.
DR   eggNOG; COG4948; Bacteria.
DR   HOGENOM; CLU_030273_1_0_4; -.
DR   OMA; HFVISQP; -.
DR   OrthoDB; 743369at2; -.
DR   Proteomes; UP000001739; Chromosome 2.
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..392
FT                   /note="L-rhamnonate dehydratase"
FT                   /id="PRO_0000351688"
FT   ACT_SITE        318
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         22
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         48
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         214
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         240
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         268
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   BINDING         338
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   SITE            291
FT                   /note="Increases basicity of active site His"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT   SITE            338
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
SQ   SEQUENCE   392 AA;  43926 MW;  6B76721E3608877A CRC64;
     MAMPTIRHVR AFIVRGGGAD YHDQPGGHWI DDHISTPMAR YPEYRQSRQS FGINVLGTLV
     VEIEASDGTV GFAVTTGGEI GAFIVEKHLA RFLEGQLVTD IEKMWDQMYF STLYYGRKGV
     VLNTISGVDL ALWDLLAKVR KEPVYQLLGG PVRDELVFYA TGARPDLAKE MGFIGGKLPL
     QHGPAEGEAG LKQNLEKLAD MRSRVGDDFW LMYDCWMSLD VPYATRLAQA AHEYGLKWIE
     ECLPPDDYWG YAELRRNVPR GMMVSTGEHE ATRWGFRMLL EMQCCDLIQP DVGWCGGITE
     LIKISALADA HNVMVVPHGS SVYSYHFVVT RHNSPFAEFL MMAPKADEVV PMFTPLLLDE
     PVPVNGRMKV PDTPGFGVRL NPECALVRPY PR