RHMD_AZOC5
ID RHMD_AZOC5 Reviewed; 393 AA.
AC A8I5F1;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 1.
DT 03-AUG-2022, entry version 86.
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=AZC_2271;
OS Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / JCM 20966 / LMG
OS 6465 / NBRC 14845 / NCIMB 13405 / ORS 571).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Xanthobacteraceae; Azorhizobium.
OX NCBI_TaxID=438753;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43989 / DSM 5975 / JCM 20966 / LMG 6465 / NBRC 14845 / NCIMB
RC 13405 / ORS 571;
RA Lee K.B., Backer P.D., Aono T., Liu C.T., Suzuki S., Suzuki T., Kaneko T.,
RA Yamada M., Tabata S., Kupfer D.M., Najar F.Z., Wiley G.B., Roe B.,
RA Binnewies T., Ussery D., Vereecke D., Gevers D., Holsters M., Oyaizu H.;
RT "Complete genome sequence of the nitrogen-fixing bacterium Azorhizobium
RT caulinodans ORS571.";
RL Submitted (APR-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}.
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DR EMBL; AP009384; BAF88269.1; -; Genomic_DNA.
DR RefSeq; WP_012170798.1; NC_009937.1.
DR AlphaFoldDB; A8I5F1; -.
DR SMR; A8I5F1; -.
DR STRING; 438753.AZC_2271; -.
DR PRIDE; A8I5F1; -.
DR EnsemblBacteria; BAF88269; BAF88269; AZC_2271.
DR KEGG; azc:AZC_2271; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_1_0_5; -.
DR OMA; HFVISQP; -.
DR OrthoDB; 743369at2; -.
DR Proteomes; UP000000270; 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; 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 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..393
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351681"
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 393 AA; 44053 MW; C2D95D2E333836CF CRC64;
MSVPTIREVR AYVVRGGGGD YHDQQGTHWI DDHIATPMSK YPAYRQSRRT FGINVLGTLV
VEVEASDGTV GFAVTTGGEP AAWIVEKHLA RFIEGAKITD IELMWDQMYR STLYYGRKGL
VVNTISGVDL ALWDLLAKWR KEPVYHLLGG AVRDELQFYA TGARPDLAKE MGFIGGKMAL
HHGPAEGEEG LRKNLDILND MRNKVGKDFW LMQDCWMALD VEYATRFSTI AWNEMGLKWT
EEALPPDDYW GYAALKKNAP KGHLITTGEH EATRWGFKML LDMECCDIIQ PDVGWCGGIT
ELIKITALAD AAGVLVVPHG SSVYSYHFVI TRHNSPFAEF LMMHPVPDQV VPMFTPLLLD
EPVPVNGRLK LDDTPGFGVR LNPECKLSRP YTH
