RHMD_SALPA
ID RHMD_SALPA Reviewed; 405 AA.
AC Q5PIM9;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 04-JAN-2005, sequence version 1.
DT 03-AUG-2022, entry version 95.
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=SPA0572;
OS Salmonella paratyphi A (strain ATCC 9150 / SARB42).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=295319;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9150 / SARB42;
RX PubMed=15531882; DOI=10.1038/ng1470;
RA McClelland M., Sanderson K.E., Clifton S.W., Latreille P., Porwollik S.,
RA Sabo A., Meyer R., Bieri T., Ozersky P., McLellan M., Harkins C.R.,
RA Wang C., Nguyen C., Berghoff A., Elliott G., Kohlberg S., Strong C., Du F.,
RA Carter J., Kremizki C., Layman D., Leonard S., Sun H., Fulton L., Nash W.,
RA Miner T., Minx P., Delehaunty K., Fronick C., Magrini V., Nhan M.,
RA Warren W., Florea L., Spieth J., Wilson R.K.;
RT "Comparison of genome degradation in Paratyphi A and Typhi, human-
RT restricted serovars of Salmonella enterica that cause typhoid.";
RL Nat. Genet. 36:1268-1274(2004).
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; CP000026; AAV76574.1; -; Genomic_DNA.
DR AlphaFoldDB; Q5PIM9; -.
DR SMR; Q5PIM9; -.
DR EnsemblBacteria; AAV76574; AAV76574; SPA0572.
DR KEGG; spt:SPA0572; -.
DR HOGENOM; CLU_030273_1_0_6; -.
DR OMA; HFVISQP; -.
DR Proteomes; UP000008185; 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; 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..405
FT /note="L-rhamnonate dehydratase"
FT /id="PRO_0000351704"
FT ACT_SITE 329
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 33
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 59
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 226
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 280
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT SITE 302
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
FT SITE 349
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01288"
SQ SEQUENCE 405 AA; 44577 MW; B61878034ACC3BD8 CRC64;
MENIMTLPKI KHVRAWFIGG ATAEKGAGGG DYHDQGGNHW IDDHIATPMS KYRDYEQSRQ
SFGINVLGTL IVEVEAENGQ TGFAVSTAGE MGCFIVEKHL NRFIEGKCVS DIKLIHDQML
GATMYYSGSG GLVMNTISCV DLALWDLFGK VVGLPVYKLL GGAVRDEIQF YATGARPDLA
KEMGFIGGKM PAHWGPHDGD AGIRKDAAMV ADMREKCGPD FWLMLDCWMS QDVNYATKLA
HACAPFNLKW IEECLPPQQY EGYRELKRNA PAGMMVTSGE HHGTLQSFRT LAETGIDIMQ
PDVGWCGGLT TLVEIAALAK SRGQLVVPHG SSVYSHHAVI TFTNTPFSEF LMTSPDCSTL
RPQFDPILLD EPVPVNGRIH KSVLDKPGFG VELNRDCHLK RPYSH
