RHMD_PARXL
ID RHMD_PARXL Reviewed; 392 AA.
AC Q13LW5;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 101.
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=Bxeno_B1956;
GN ORFNames=Bxe_B1030;
OS Paraburkholderia xenovorans (strain LB400).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=266265;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LB400;
RX PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT shaped for versatility.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006).
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP000271; ABE34924.1; -; Genomic_DNA.
DR RefSeq; WP_011492233.1; NZ_CP008762.1.
DR AlphaFoldDB; Q13LW5; -.
DR SMR; Q13LW5; -.
DR STRING; 266265.Bxe_B1030; -.
DR EnsemblBacteria; ABE34924; ABE34924; Bxe_B1030.
DR KEGG; bxb:DR64_6351; -.
DR KEGG; bxe:Bxe_B1030; -.
DR PATRIC; fig|266265.5.peg.6734; -.
DR eggNOG; COG4948; Bacteria.
DR OMA; HFVISQP; -.
DR OrthoDB; 743369at2; -.
DR Proteomes; UP000001817; 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; Reference proteome.
FT CHAIN 1..392
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351689"
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; 43883 MW; 3EC93D19A6327F0F CRC64;
MAMPTIRHVR AFIVRGGGAD YHDQPGGHWI DDHISTPMAR YPEYRQSRQS FGINVLGTLV
VEIEASDGTV GFAVTTGGEI GAFIVEKHLA RFLEGQLVTD IEKMWDQMYF STLYYGRKGV
VLNTISGVDL ALWDLLAKVR KEPVYQLLGG PVRDELVFYA TGARPDLAKE MGFIGGKLPL
QHGPAEGDAG LRQNLDKLAE MRSRVGDDFW LMYDCWMSLD VPYATRLAQA AHEYGLKWIE
ECLPPDDYWG YAELRRNVPR GMMVSTGEHE ATRWGFRMLL EMQCCDLIQP DVGWCGGITE
LIKISALADA HNVMVVPHGS SVYSYHFVVT RHNSPFAEFL MMAPKADEVV PMFTPLLLDE
PVPVNGRMKV PDAPGFGVRL NPECALVRPY AR
