RHMD_SALTY
ID RHMD_SALTY Reviewed; 405 AA.
AC Q8ZNF9;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=L-rhamnonate dehydratase;
DE Short=RhamD;
DE EC=4.2.1.90;
GN Name=rhmD; Synonyms=yfaW; OrderedLocusNames=STM2291;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND
RP SUBSTRATE ANALOG, FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, KINETIC
RP PARAMETERS, SUBUNIT, CATALYTIC MECHANISM, AND REACTION STEREOCHEMISTRY.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=18754693; DOI=10.1021/bi800914r;
RA Rakus J.F., Fedorov A.A., Fedorov E.V., Glasner M.E., Hubbard B.K.,
RA Delli J.D., Babbitt P.C., Almo S.C., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate
RT dehydratase.";
RL Biochemistry 47:9944-9954(2008).
CC -!- FUNCTION: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-
CC L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate,
CC although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.
CC {ECO:0000269|PubMed:18754693}.
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;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:18754693};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:18754693};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.25 mM for L-rhamnonate {ECO:0000269|PubMed:18754693};
CC KM=1.6 mM for L-lyxonate {ECO:0000269|PubMed:18754693};
CC KM=0.06 mM for L-mannonate {ECO:0000269|PubMed:18754693};
CC Note=The catalytic efficiency observed with L-rhamnonate as substrate
CC is 533- and 8-fold higher than that observed with L-lyxonate and L-
CC mannonate, respectively.;
CC -!- SUBUNIT: Homooctamer; tetramer of dimers.
CC {ECO:0000269|PubMed:18754693}.
CC -!- MISCELLANEOUS: Reaction proceeds via a syn dehydration.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. RhamD subfamily. {ECO:0000305}.
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DR EMBL; AE006468; AAL21192.1; -; Genomic_DNA.
DR RefSeq; NP_461233.1; NC_003197.2.
DR RefSeq; WP_000427827.1; NC_003197.2.
DR PDB; 2GSH; X-ray; 2.39 A; A/B=2-405.
DR PDB; 2P3Z; X-ray; 1.80 A; A/B=2-405.
DR PDB; 3BOX; X-ray; 1.80 A; A/B=2-405.
DR PDB; 3CXO; X-ray; 2.00 A; A/B=2-405.
DR PDB; 3D46; X-ray; 1.90 A; A/B/C/D/E/F/G/H=1-405.
DR PDB; 3D47; X-ray; 1.80 A; A/B/C/D/E/F/G/H=1-405.
DR PDBsum; 2GSH; -.
DR PDBsum; 2P3Z; -.
DR PDBsum; 3BOX; -.
DR PDBsum; 3CXO; -.
DR PDBsum; 3D46; -.
DR PDBsum; 3D47; -.
DR AlphaFoldDB; Q8ZNF9; -.
DR SMR; Q8ZNF9; -.
DR STRING; 99287.STM2291; -.
DR PaxDb; Q8ZNF9; -.
DR DNASU; 1253813; -.
DR EnsemblBacteria; AAL21192; AAL21192; STM2291.
DR GeneID; 1253813; -.
DR KEGG; stm:STM2291; -.
DR PATRIC; fig|99287.12.peg.2425; -.
DR HOGENOM; CLU_030273_1_0_6; -.
DR OMA; HFVISQP; -.
DR PhylomeDB; Q8ZNF9; -.
DR BioCyc; SENT99287:STM2291-MON; -.
DR BRENDA; 4.2.1.90; 5542.
DR EvolutionaryTrace; Q8ZNF9; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0016836; F:hydro-lyase activity; IBA:GO_Central.
DR GO; GO:0050032; F:L-rhamnonate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0016052; P:carbohydrate catabolic process; IBA:GO_Central.
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 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..405
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351707"
FT ACT_SITE 329
FT /note="Proton acceptor"
FT BINDING 33
FT /ligand="substrate"
FT BINDING 59
FT /ligand="substrate"
FT BINDING 226
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 280
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 349
FT /ligand="substrate"
FT SITE 302
FT /note="Increases basicity of active site His"
FT SITE 349
FT /note="Transition state stabilizer"
FT STRAND 9..20
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 40..42
FT /evidence="ECO:0007829|PDB:2P3Z"
FT TURN 48..51
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:2P3Z"
FT TURN 63..65
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 69..76
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 81..87
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 89..98
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 101..104
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 112..123
FT /evidence="ECO:0007829|PDB:2P3Z"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 132..152
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 156..159
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 164..175
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 177..183
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 199..217
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 219..226
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 233..243
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 250..252
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 260..269
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 275..278
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 285..293
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 297..299
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 303..306
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 309..321
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 332..339
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 348..351
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:2P3Z"
FT TURN 363..367
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 378..380
FT /evidence="ECO:0007829|PDB:2P3Z"
FT HELIX 381..384
FT /evidence="ECO:0007829|PDB:2P3Z"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:2P3Z"
SQ SEQUENCE 405 AA; 44706 MW; 69787FA29E2939E5 CRC64;
MENIMTLPKI KHVRAWFIGG ATAEKGAGGG DYHDQGGNHW IDDHIATPMS KYRDYEQSRQ
SFGINVLGTL IVEVEAENRQ TGFAVSTAGE MGCFIVEKHL NRFIEGKCVS DIKLIHDQML
GATMYYSGSG GLVMNTISCV DLALWDLFGK VVGLPVYKLL GGAVRDEIQF YATGARPDLA
KEMGFIGGKM PTHWGPHDGD AGIRKDAAMV ADMREKCGPD FWLMLDCWMS QDVNYATKLA
HACAPFNLKW IEECLPPQQY EGYRELKRNA PAGMMVTSGE HHGTLQSFRT LAETGIDIMQ
PDVGWCGGLT TLVEIAALAK SRGQLVVPHG SSVYSHHAVI TFTNTPFSEF LMTSPDCSTL
RPQFDPILLD EPVPVNGRIH KSVLDKPGFG VELNRDCHLK RPYSH
