ID A0A0F3L9D3_9CAUL Unreviewed; 397 AA.
AC A0A0F3L9D3;
DT 24-JUN-2015, integrated into UniProtKB/TrEMBL.
DT 24-JUN-2015, sequence version 1.
DT 24-JAN-2024, entry version 31.
DE RecName: Full=L-rhamnonate dehydratase {ECO:0000256|HAMAP-Rule:MF_01288};
DE Short=RhamD {ECO:0000256|HAMAP-Rule:MF_01288};
DE EC=4.2.1.90 {ECO:0000256|HAMAP-Rule:MF_01288};
GN Name=rhmD {ECO:0000256|HAMAP-Rule:MF_01288};
GN ORFNames=VH88_12025 {ECO:0000313|EMBL:KJV40108.1};
OS Brevundimonas sp. KM4.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Brevundimonas.
OX NCBI_TaxID=1628191 {ECO:0000313|EMBL:KJV40108.1, ECO:0000313|Proteomes:UP000033583};
RN [1] {ECO:0000313|EMBL:KJV40108.1, ECO:0000313|Proteomes:UP000033583}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KM4 {ECO:0000313|EMBL:KJV40108.1,
RC ECO:0000313|Proteomes:UP000033583};
RA Sulaiman J., Priya K., Chan K.-G.;
RT "Draft genome sequence of Brevundimonas sp. KM4.";
RL Submitted (MAR-2015) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-
CC L-rhamnonate (KDR). {ECO:0000256|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:0000256|HAMAP-
CC Rule:MF_01288};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01288};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|HAMAP-Rule:MF_01288};
CC -!- SUBUNIT: Homooctamer; tetramer of dimers. {ECO:0000256|HAMAP-
CC Rule:MF_01288}.
CC -!- MISCELLANEOUS: Reaction proceeds via a syn dehydration.
CC {ECO:0000256|HAMAP-Rule:MF_01288}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. RhamD subfamily. {ECO:0000256|HAMAP-Rule:MF_01288}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KJV40108.1}.
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DR EMBL; JZRG01000021; KJV40108.1; -; Genomic_DNA.
DR RefSeq; WP_045811464.1; NZ_JZRG01000021.1.
DR AlphaFoldDB; A0A0F3L9D3; -.
DR PATRIC; fig|1628191.3.peg.1099; -.
DR Proteomes; UP000033583; Unassembled WGS sequence.
DR GO; GO:0050032; F:L-rhamnonate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
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; 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; SFLDG00179; mandelate_racemase; 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.
PE 3: Inferred from homology;
KW Lyase {ECO:0000256|HAMAP-Rule:MF_01288};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_01288};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01288}.
FT DOMAIN 170..266
FT /note="Mandelate racemase/muconate lactonizing enzyme C-
FT terminal"
FT /evidence="ECO:0000259|SMART:SM00922"
FT ACT_SITE 323
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 27
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 53
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 219
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 245
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 273
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 343
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT SITE 296
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT SITE 343
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
SQ SEQUENCE 397 AA; 44252 MW; C8EB2C0905C3B40F CRC64;
MSRLPRIKHV RAFVVKNDGT GGGADYHDQG DGHWIDDHIA TPMARYPEYR QSRRSFGINV
LGTLVVEIEA ENGVVGFAVT TGGEPAAYIV EKHLARFLEG RDPAEVEKIW DQMYFSTQYY
GRKGLVVNAI SGVDLALWDL LGRLRQEPVF AMLGGAVRDE LTFYATGARP DKAKELGFIG
GKMPLHHGPA EGEEGLHKTI AELEAMRNAC GDDFWLMFDC WMALDLNYAT RLAHEAHKLG
LKWIEEALSP DDYWGYQALK KNAPKGMLVT TGEHEATRWG FRMLLEMECC DIIQPDVGWC
GGVTELQKIS ALADAKGVLM IPHGSSVYSY HFVVTRHNSP FAEFLMMAPD ADEVVPMFHP
QLIGEPVPVN GRLKVPDTPG FGVELNRDIA LHRPYAR
//
