RHMD_DELAS
ID RHMD_DELAS Reviewed; 395 AA.
AC A9BQY2;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 2.
DT 03-AUG-2022, entry version 70.
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=Daci_0291;
OS Delftia acidovorans (strain DSM 14801 / SPH-1).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Delftia.
OX NCBI_TaxID=398578;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14801 / SPH-1;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Lowry S., Clum A., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Kim E., Schleheck D., Richardson P.;
RT "Complete sequence of Delftia acidovorans DSM 14801 / SPH-1.";
RL Submitted (NOV-2007) 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=ABX32937.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000884; ABX32937.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_016452099.1; NC_010002.1.
DR AlphaFoldDB; A9BQY2; -.
DR SMR; A9BQY2; -.
DR STRING; 398578.Daci_0291; -.
DR PRIDE; A9BQY2; -.
DR EnsemblBacteria; ABX32937; ABX32937; Daci_0291.
DR KEGG; dac:Daci_0291; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_1_0_4; -.
DR Proteomes; UP000000784; 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; Reference proteome.
FT CHAIN 1..395
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351690"
FT ACT_SITE 319
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 23
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 49
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 215
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 395 AA; 43944 MW; 96CD5CB9833E4E1F CRC64;
MTQIPTIKQV RAFTLKGGGA DYHDQSDGHW IDDHIATPMA KYPEYRQSRR SFGINVLGTL
VVEIEDSAGR VGFAVTTGGE PAAYIVEKHL ARFLEGARVT DIERIWDQMY LSTLYYGRKG
IVINTISGVD LALWDLLGKV RGEPVHQLLG GAVRDELQFY ATGARPDLAQ KMGFIGGKMP
LHHGPAEGEE GLRRNLQELA TMRERVGPDF WLMLDCWMSL DVNYATRLAQ GAQAHGLKWI
EEALPPDDYW GYAALRKNVP TGMLVTTGEH EATRWGFRQL LEMGCCDIIQ PDVGWCGGIT
ELLKISALAD AHQALVIPHG SSVYSYHFVA TRHNSPFAEF LMMAPKADEV VPMFHPQLLG
EPVPVNGRMR LSALDRPGFG VELNPECALH RPYTH
