FUCD_XANCP
ID FUCD_XANCP Reviewed; 441 AA.
AC Q8P3K2;
DT 05-SEP-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=L-fuconate dehydratase {ECO:0000303|PubMed:17144652};
DE Short=FucD {ECO:0000303|PubMed:17144652};
DE EC=4.2.1.68 {ECO:0000269|PubMed:17144652, ECO:0000303|PubMed:17144652};
GN OrderedLocusNames=XCC4069;
OS Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB
OS 528 / LMG 568 / P 25).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xanthomonas.
OX NCBI_TaxID=190485;
RN [1] {ECO:0000312|EMBL:AAM43290.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25;
RX PubMed=12024217; DOI=10.1038/417459a;
RA da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R.,
RA Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr.,
RA Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G.,
RA Cannavan F., Cardozo J., Chambergo F., Ciapina L.P., Cicarelli R.M.B.,
RA Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B.,
RA Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F.,
RA Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T.,
RA Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A.,
RA Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J.,
RA Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M.,
RA Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A.,
RA Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A.,
RA Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M.,
RA Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P.;
RT "Comparison of the genomes of two Xanthomonas pathogens with differing host
RT specificities.";
RL Nature 417:459-463(2002).
RN [2] {ECO:0000312|PDB:1YEY}
RP X-RAY CRYSTALLOGRAPHY (2.34 ANGSTROMS) IN COMPLEX WITH MAGNESIUM.
RA Fedorov A.A., Fedorov E.V., Yew W.S., Gerlt J.A., Almo S.C.;
RT "Crystal structure of L-fuconate dehydratase from Xanthomonas campestris
RT pv. campestris str. ATCC 33913.";
RL Submitted (DEC-2004) to the PDB data bank.
RN [3] {ECO:0000305, ECO:0000312|PDB:2HXT}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-220 IN
RP COMPLEXES WITH MAGNESIUM; D-ERYTHRONOHYDROXAMATE AND L-FUCONATE, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP MUTAGENESIS OF LYS-220.
RC STRAIN=ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25
RC {ECO:0000269|PubMed:17144652};
RX PubMed=17144652; DOI=10.1021/bi061687o;
RA Yew W.S., Fedorov A.A., Fedorov E.V., Rakus J.F., Pierce R.W., Almo S.C.,
RA Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: L-fuconate
RT dehydratase from Xanthomonas campestris.";
RL Biochemistry 45:14582-14597(2006).
CC -!- FUNCTION: Plays a role in the catabolism of L-fucose. Catalyzes the
CC dehydration of L-fuconate to 2-keto-3-deoxy-L-fuconate by the
CC abstraction of the 2-proton to generate an enediolate intermediate that
CC is stabilized by the magnesium ion. L-fuconate is the preferred
CC substrate with 15-fold lower activity observed for L-galactonate and 8-
CC fold lower activity with D-arabinonate. No activity detected with D-
CC fuconate. Can also catalyze the epimerization of L-talonate and D-
CC ribonate, but at slow rates. {ECO:0000269|PubMed:17144652}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-fuconate = 2-dehydro-3-deoxy-L-fuconate + H2O;
CC Xref=Rhea:RHEA:22772, ChEBI:CHEBI:15377, ChEBI:CHEBI:21291,
CC ChEBI:CHEBI:37448; EC=4.2.1.68;
CC Evidence={ECO:0000269|PubMed:17144652};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:17144652};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:17144652};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.03 mM for L-fuconate {ECO:0000269|PubMed:17144652};
CC KM=6.2 mM for L-galactonate {ECO:0000269|PubMed:17144652};
CC KM=2.1 mM for D-arabinonate {ECO:0000269|PubMed:17144652};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17144652, ECO:0000269|Ref.2}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; AE008922; AAM43290.1; -; Genomic_DNA.
DR RefSeq; NP_639408.1; NC_003902.1.
DR RefSeq; WP_011039138.1; NC_003902.1.
DR PDB; 1YEY; X-ray; 2.34 A; A/B/C/D=1-441.
DR PDB; 2HNE; X-ray; 2.00 A; A/B/C/D=1-436.
DR PDB; 2HXT; X-ray; 1.70 A; A=1-441.
DR PDB; 2HXU; X-ray; 1.80 A; A=1-441.
DR PDBsum; 1YEY; -.
DR PDBsum; 2HNE; -.
DR PDBsum; 2HXT; -.
DR PDBsum; 2HXU; -.
DR AlphaFoldDB; Q8P3K2; -.
DR SMR; Q8P3K2; -.
DR STRING; 340.xcc-b100_4271; -.
DR EnsemblBacteria; AAM43290; AAM43290; XCC4069.
DR KEGG; xcc:XCC4069; -.
DR PATRIC; fig|190485.4.peg.4361; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_2_0_6; -.
DR OMA; SGAIDVC; -.
DR BioCyc; MetaCyc:MON-21810; -.
DR SABIO-RK; Q8P3K2; -.
DR EvolutionaryTrace; Q8P3K2; -.
DR Proteomes; UP000001010; Chromosome.
DR GO; GO:0016836; F:hydro-lyase activity; IBA:GO_Central.
DR GO; GO:0050023; F:L-fuconate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0016052; P:carbohydrate catabolic process; IDA:UniProtKB.
DR CDD; cd03324; rTSbeta_L-fuconate_dehydratase; 1.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR034610; L-fuconate_dehydratase.
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; SFLDF00111; L-fuconate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..441
FT /note="L-fuconate dehydratase"
FT /id="PRO_0000418813"
FT ACT_SITE 220
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17144652"
FT ACT_SITE 351
FT /evidence="ECO:0000255"
FT BINDING 22..24
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 32
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 218
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17144652, ECO:0000269|Ref.2"
FT BINDING 250
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 274
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17144652, ECO:0000269|Ref.2"
FT BINDING 274
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 301
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17144652, ECO:0000269|Ref.2"
FT BINDING 301
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 351..353
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT BINDING 382
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17144652"
FT MUTAGEN 220
FT /note="K->A: Inactive."
FT /evidence="ECO:0000269|PubMed:17144652"
FT STRAND 3..13
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:2HXT"
FT TURN 19..22
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 33..43
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 60..68
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 71..74
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 79..84
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 86..94
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 97..101
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 107..127
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 132..137
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 141..147
FT /evidence="ECO:0007829|PDB:2HXT"
FT TURN 154..156
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 159..169
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 173..183
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 185..193
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 199..211
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 215..220
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 225..239
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 241..248
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 255..263
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 266..268
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 270..274
FT /evidence="ECO:0007829|PDB:2HXU"
FT HELIX 282..292
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 297..299
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 306..315
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 319..321
FT /evidence="ECO:0007829|PDB:2HXT"
FT TURN 325..327
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 330..343
FT /evidence="ECO:0007829|PDB:2HXT"
FT TURN 354..356
FT /evidence="ECO:0007829|PDB:2HNE"
FT HELIX 357..371
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 381..383
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 388..390
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 391..393
FT /evidence="ECO:0007829|PDB:2HXT"
FT STRAND 397..402
FT /evidence="ECO:0007829|PDB:1YEY"
FT STRAND 407..409
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 416..422
FT /evidence="ECO:0007829|PDB:2HXT"
FT TURN 424..426
FT /evidence="ECO:0007829|PDB:2HXT"
FT HELIX 428..434
FT /evidence="ECO:0007829|PDB:2HXT"
SQ SEQUENCE 441 AA; 48124 MW; 4BAF5BEC1D1E3327 CRC64;
MRTIIALETH DVRFPTSREL DGSDAMNPDP DYSAAYVVLR TDGAEDLAGY GLVFTIGRGN
DVQTAAVAAL AEHVVGLSVD KVIADLGAFA RRLTNDSQLR WLGPEKGVMH MAIGAVINAA
WDLAARAANK PLWRFIAELT PEQLVDTIDF RYLSDALTRD EALAILRDAQ PQRAARTATL
IEQGYPAYTT SPGWLGYSDE KLVRLAKEAV ADGFRTIKLK VGANVQDDIR RCRLARAAIG
PDIAMAVDAN QRWDVGPAID WMRQLAEFDI AWIEEPTSPD DVLGHAAIRQ GITPVPVSTG
EHTQNRVVFK QLLQAGAVDL IQIDAARVGG VNENLAILLL AAKFGVRVFP HAGGVGLCEL
VQHLAMADFV AITGKMEDRA IEFVDHLHQH FLDPVRIQHG RYLAPEVPGF SAEMHPASIA
EFSYPDGRFW VEDLAASKAK A
