RHMD_PARP8
ID RHMD_PARP8 Reviewed; 392 AA.
AC B2JLI8;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 1.
DT 03-AUG-2022, entry version 79.
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=Bphy_3468;
OS Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 /
OS STM815) (Burkholderia phymatum).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=391038;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 17167 / CIP 108236 / LMG 21445 / STM815;
RX PubMed=25197461; DOI=10.4056/sigs.4861021;
RA Moulin L., Klonowska A., Caroline B., Booth K., Vriezen J.A., Melkonian R.,
RA James E.K., Young J.P., Bena G., Hauser L., Land M., Kyrpides N., Bruce D.,
RA Chain P., Copeland A., Pitluck S., Woyke T., Lizotte-Waniewski M.,
RA Bristow J., Riley M.;
RT "Complete genome sequence of Burkholderia phymatum STM815(T), a broad host
RT range and efficient nitrogen-fixing symbiont of Mimosa species.";
RL Stand. Genomic Sci. 9:763-774(2014).
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; CP001044; ACC72621.1; -; Genomic_DNA.
DR RefSeq; WP_012402794.1; NZ_CADFGH010000006.1.
DR AlphaFoldDB; B2JLI8; -.
DR SMR; B2JLI8; -.
DR STRING; 391038.Bphy_3468; -.
DR EnsemblBacteria; ACC72621; ACC72621; Bphy_3468.
DR KEGG; bph:Bphy_3468; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_1_0_4; -.
DR OMA; HFVISQP; -.
DR OrthoDB; 743369at2; -.
DR Proteomes; UP000001192; 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_0000351687"
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; 43927 MW; 64ACC3B4117CA0FD CRC64;
MAMPSIRHVR AFVVRGGGAD YHDQADGHWI DDHISTPMAR YPEYRQSRQS FGINVLGTLV
VEIEASDGTV GFAVTTGGEI GAFIVEKHLA RFLEGQLVTD IEKMWDQMYF STLYYGRKGV
VLNTISGVDL ALWDLLAKVR KEPVYQLLGG PVRDELQFYA TGARPDLAKE MGFIGGKLPL
QHSPAEGEEG LRKNIDKLAE MRGRVGGDFW LMYDCWMSLD VTYATKLAKA AHEHGLKWIE
EALPPDDYWG YAELRRNVPR GMMVSTGEHE ATRWGFRMLL EMGCCDLIQP DVGWCGGITE
LVKISALADA HNVLVVPHGS SVYSYHFVVT RHNSPFAEFL MMAPKADQVV PMFTPLLLDE
PVPVNGRMRV PDTPGFGVRL NPECKLERPY QH
