RHMD_BURCM
ID RHMD_BURCM Reviewed; 392 AA.
AC Q0BA70;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 89.
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=Bamb_3399;
OS Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) (Burkholderia cepacia
OS (strain AMMD)).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX NCBI_TaxID=339670;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-244 / AMMD;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Pitluck S., Bruce D., Chain P.,
RA Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Kim E., Parke J., Coenye T., Konstantinidis K.,
RA Ramette A., Tiedje J., Richardson P.;
RT "Complete sequence of chromosome 2 of Burkholderia cepacia AMMD.";
RL Submitted (AUG-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}.
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DR EMBL; CP000441; ABI88953.1; -; Genomic_DNA.
DR RefSeq; WP_011658428.1; NZ_CP009799.1.
DR AlphaFoldDB; Q0BA70; -.
DR SMR; Q0BA70; -.
DR STRING; 339670.Bamb_3399; -.
DR EnsemblBacteria; ABI88953; ABI88953; Bamb_3399.
DR GeneID; 44694045; -.
DR KEGG; bam:Bamb_3399; -.
DR PATRIC; fig|339670.21.peg.3611; -.
DR eggNOG; COG4948; Bacteria.
DR OMA; HFVISQP; -.
DR Proteomes; UP000000662; 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_0000351682"
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; 43796 MW; 6FD2EF60641A3F02 CRC64;
MSMPTIRAVR ALTVRGGGAD YHDQDAGHWI DDHIATPMSR YPEYRQSRQS FGINVLGTLV
IEIEASDGTV GFAVTTGGEI GAFIVERHLA RFIEGQRVTD IEKMWDQMFY ATLYYGRKGV
VLNAISGVDL ALWDLLGKVR QEPVHQLLGG KVRDELEFYA TGARPDLAKE MGFIGGKLPL
HHGPAEGDAG LRRNLDALAD MRSRVGDDFW LMLDCWMSLD VPYATRLAHG AHALGLKWIE
ECLPPDDYWG YAKLRRDVPR GMLVTTGEHE ATRWGFRMLL EMECCDIIQP DVGWCGGLTE
LMRISALADA RGVLVIPHGS SVYSYHFVAT RHNSPFAEFL MMAPQADRVV PMFDPLLLDE
PVPVGGRMKV PDTAGFGVRL NPDVRMQRPY EH
