ID A0A0N1BDG9_9SPHN Unreviewed; 406 AA.
AC A0A0N1BDG9;
DT 09-DEC-2015, integrated into UniProtKB/TrEMBL.
DT 09-DEC-2015, sequence version 1.
DT 24-JAN-2024, entry version 24.
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=IP68_19045 {ECO:0000313|EMBL:KPF71449.1};
OS Blastomonas sp. AAP25.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Blastomonas.
OX NCBI_TaxID=1523416 {ECO:0000313|EMBL:KPF71449.1, ECO:0000313|Proteomes:UP000037930};
RN [1] {ECO:0000313|EMBL:KPF71449.1, ECO:0000313|Proteomes:UP000037930}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AAP25 {ECO:0000313|EMBL:KPF71449.1,
RC ECO:0000313|Proteomes:UP000037930};
RA Zeng Y., Feng F., Liu Y., Koblizek M.;
RT "Novel Diversity of Limnic Aerobic Anoxygenic Phototrophic Bacteria as
RT Revealed by High-throughput Strain Identification and Genome Sequencing.";
RL Submitted (AUG-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:KPF71449.1}.
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DR EMBL; LJHP01000046; KPF71449.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0N1BDG9; -.
DR PATRIC; fig|1523416.3.peg.2831; -.
DR Proteomes; UP000037930; 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 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; 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.
DR PROSITE; PS00908; MR_MLE_1; 1.
PE 3: Inferred from homology;
KW Lyase {ECO:0000256|HAMAP-Rule:MF_01288};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01288};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01288}; Reference proteome {ECO:0000313|Proteomes:UP000037930}.
FT DOMAIN 177..273
FT /note="Mandelate racemase/muconate lactonizing enzyme C-
FT terminal"
FT /evidence="ECO:0000259|SMART:SM00922"
FT ACT_SITE 330
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 34
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 60
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 226
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 280
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT BINDING 350
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT SITE 303
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
FT SITE 350
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01288"
SQ SEQUENCE 406 AA; 45006 MW; 52FADBC8FE0AD49F CRC64;
MFARRGRCRS VVIPFPKIVA VRAFTARGGG ADYHDQGAGH WIDDHIATPM ARYPEYRASR
QSFGINVLGT LVVELEASDG TVGFAVTTGG EPAAFIVERH LSRFLIGQNP ADFERIWDQM
YFSTQYYGRK GLVVNAISAV DLALWDLLGK LRQEPVYHLL GGAVRDELQF YATGARPDIA
RDLGFIGGKL PLHHGPAEGD EGLKKNVALL ADMRARCGDD FWLMHDCWMA LDVDYATRLA
HACHAHGLKW IEEAISPDDY WGYAELKRNV PNGMLVTCGE HEATRWGFRM LLEMDCCDII
QPDVGWCGGI TELIKISALA DARGKLVVPH GSSVYSYHFV VTRHNSPFAE FLMMHPGPTE
VVPMFAPQLL GEPVPHNGRI KASALDKPGF GVELNPDVPL HRPYSN
//
