ID RHMD_SALPB Reviewed; 405 AA.
AC A9N5C2;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 2.
DT 13-SEP-2023, entry version 76.
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=SPAB_00692;
OS Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=1016998;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1250 / SPB7;
RG The Salmonella enterica serovar Paratyphi B Genome Sequencing Project;
RA McClelland M., Sanderson E.K., Porwollik S., Spieth J., Clifton W.S.,
RA Fulton R., Cordes M., Wollam A., Shah N., Pepin K., Bhonagiri V., Nash W.,
RA Johnson M., Thiruvilangam P., Wilson R.;
RL Submitted (NOV-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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABX66118.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000886; ABX66118.1; ALT_INIT; Genomic_DNA.
DR AlphaFoldDB; A9N5C2; -.
DR SMR; A9N5C2; -.
DR KEGG; spq:SPAB_00692; -.
DR PATRIC; fig|1016998.12.peg.651; -.
DR HOGENOM; CLU_030273_1_0_6; -.
DR BioCyc; SENT1016998:SPAB_RS02880-MONOMER; -.
DR Proteomes; UP000008556; 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:amino acid catabolic process; IEA:InterPro.
DR CDD; cd03327; MR_like_2; 1.
DR Gene3D; 3.20.20.120; Enolase-like C-terminal domain; 1.
DR Gene3D; 3.30.390.10; Enolase-like, N-terminal domain; 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 InterPro; IPR046945; RHMD-like.
DR PANTHER; PTHR13794; ENOLASE SUPERFAMILY, MANDELATE RACEMASE; 1.
DR PANTHER; PTHR13794:SF58; MITOCHONDRIAL ENOLASE SUPERFAMILY MEMBER 1; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDS00001; Enolase; 1.
DR SFLD; SFLDF00006; rhamnonate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; Enolase C-terminal domain-like; 1.
DR SUPFAM; SSF54826; Enolase N-terminal domain-like; 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_0000351705"
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; 44607 MW; 293920BC6B923523 CRC64;
MENIMTLPKI KHVRAWFIGG ATAEKGAGGG DYHDQGGNHW IDDHIATPMS KYRDYEQSRQ
SFGINVLGTL IVEVEAENGQ 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
//
