RHMD_VEREI
ID RHMD_VEREI Reviewed; 398 AA.
AC A1WFL2;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 2.
DT 03-AUG-2022, entry version 77.
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=Veis_0636;
OS Verminephrobacter eiseniae (strain EF01-2).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Verminephrobacter.
OX NCBI_TaxID=391735;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=EF01-2;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T.,
RA Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Kim E., Stahl D., Richardson P.;
RT "Complete sequence of chromosome 1 of Verminephrobacter eiseniae EF01-2.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABM56419.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000542; ABM56419.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_041950468.1; NC_008786.1.
DR AlphaFoldDB; A1WFL2; -.
DR SMR; A1WFL2; -.
DR STRING; 391735.Veis_0636; -.
DR EnsemblBacteria; ABM56419; ABM56419; Veis_0636.
DR KEGG; vei:Veis_0636; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_1_0_4; -.
DR OrthoDB; 743369at2; -.
DR Proteomes; UP000000374; 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 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; Reference proteome.
FT CHAIN 1..398
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351710"
FT ACT_SITE 319
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 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 269
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 339
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT SITE 292
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT SITE 339
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
SQ SEQUENCE 398 AA; 44240 MW; 405FF3FD65D886D0 CRC64;
MGMPFIKHVR AFTVRGGGAD YHDQGGGHWI DDHIATPMSK YPEYRQSRQS FGINVLGTLV
VEIEASDGTV GFSVTTGGDL GCFIVEKHLA RFLEGARVTD IEKMWDQMYS ATLYYGRKGI
VINTISGVDL ALWDLLAKIR KEPVHALLGG PVRDELIFYA TGARPDLARQ MGFIGGKMPL
HHAPAEREEG LAKNLDMIGD MRSKVGKDFW LMLDCWMSLD VEYATRLATA ARNEHGLKWI
EEALSPDDYW GYAELRRNVP RGMLVTTGEH EATRWGFRLL LEMGCCDIIQ PDVGWCGGIT
ELIKISNLAD AHGKLVVPHG SSVYSYHFVI TRQNSPFAEF LMMAPKADEV VPMFNPQLLD
EPVPVNGRIK ASALDAPGFG VRLNPDIALH RPYPRQAA
