XYLD_CAUVC
ID XYLD_CAUVC Reviewed; 595 AA.
AC Q9A9Z2;
DT 11-DEC-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=D-xylonate dehydratase {ECO:0000303|PubMed:27102126};
DE Short=XyDHT {ECO:0000303|PubMed:27102126};
DE EC=4.2.1.82 {ECO:0000269|PubMed:27102126};
DE AltName: Full=Gluconate dehydratase {ECO:0000305};
DE EC=4.2.1.39 {ECO:0000269|PubMed:27102126};
GN Name=xylD {ECO:0000303|PubMed:17172333};
GN OrderedLocusNames=CC_0819 {ECO:0000312|EMBL:AAK22804.1};
OS Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Caulobacter.
OX NCBI_TaxID=190650;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19089 / CB15;
RX PubMed=11259647; DOI=10.1073/pnas.061029298;
RA Nierman W.C., Feldblyum T.V., Laub M.T., Paulsen I.T., Nelson K.E.,
RA Eisen J.A., Heidelberg J.F., Alley M.R.K., Ohta N., Maddock J.R.,
RA Potocka I., Nelson W.C., Newton A., Stephens C., Phadke N.D., Ely B.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Gwinn M.L., Haft D.H., Kolonay J.F.,
RA Smit J., Craven M.B., Khouri H.M., Shetty J., Berry K.J., Utterback T.R.,
RA Tran K., Wolf A.M., Vamathevan J.J., Ermolaeva M.D., White O.,
RA Salzberg S.L., Venter J.C., Shapiro L., Fraser C.M.;
RT "Complete genome sequence of Caulobacter crescentus.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4136-4141(2001).
RN [2]
RP DISRUPTION PHENOTYPE, AND PATHWAY.
RX PubMed=17172333; DOI=10.1128/jb.01438-06;
RA Stephens C., Christen B., Fuchs T., Sundaram V., Watanabe K., Jenal U.;
RT "Genetic analysis of a novel pathway for D-xylose metabolism in Caulobacter
RT crescentus.";
RL J. Bacteriol. 189:2181-2185(2007).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, IRON-SULFUR CLUSTER,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF CYS-64; CYS-132;
RP CYS-205 AND CYS-450.
RX PubMed=27102126; DOI=10.1007/s00253-016-7530-8;
RA Andberg M., Aro-Kaerkkaeinen N., Carlson P., Oja M., Bozonnet S.,
RA Toivari M., Hakulinen N., O'Donohue M., Penttilae M., Koivula A.;
RT "Characterization and mutagenesis of two novel iron-sulphur cluster
RT pentonate dehydratases.";
RL Appl. Microbiol. Biotechnol. 100:7549-7563(2016).
RN [4]
RP CRYSTALLIZATION.
RX PubMed=27487924; DOI=10.1107/s2053230x16010311;
RA Rahman M.M., Andberg M., Koivula A., Rouvinen J., Hakulinen N.;
RT "Crystallization and X-ray diffraction analysis of an L-arabinonate
RT dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate
RT dehydratase from Caulobacter crescentus.";
RL Acta Crystallogr. F Struct. Biol. Commun. 72:604-608(2016).
RN [5] {ECO:0007744|PDB:5OYN}
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 6-595 IN COMPLEX WITH 2FE-2S AND
RP MAGNESIUM, COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC 19089 / CB15;
RX PubMed=29339766; DOI=10.1038/s41598-018-19192-6;
RA Rahman M.M., Andberg M., Koivula A., Rouvinen J., Hakulinen N.;
RT "The crystal structure of D-xylonate dehydratase reveals functional
RT features of enzymes from the Ilv/ED dehydratase family.";
RL Sci. Rep. 8:865-865(2018).
CC -!- FUNCTION: Catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy-
CC D-arabinonate during D-xylose degradation. Can also dehydrate D-
CC gluconate, with similar catalytic efficiency. Has weak activity with D-
CC galactonate, D-fuconate and L-arabinonate.
CC {ECO:0000269|PubMed:27102126}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O;
CC Xref=Rhea:RHEA:19157, ChEBI:CHEBI:15377, ChEBI:CHEBI:16699,
CC ChEBI:CHEBI:17746; EC=4.2.1.82;
CC Evidence={ECO:0000269|PubMed:27102126};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O;
CC Xref=Rhea:RHEA:21612, ChEBI:CHEBI:15377, ChEBI:CHEBI:18391,
CC ChEBI:CHEBI:57990; EC=4.2.1.39;
CC Evidence={ECO:0000269|PubMed:27102126};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:29339766, ECO:0000305|PubMed:27102126};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27102126, ECO:0000269|PubMed:29339766};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.9 mM for D-xylonate {ECO:0000269|PubMed:27102126};
CC KM=4.0 mM for D-gluconate {ECO:0000269|PubMed:27102126};
CC KM=7.8 mM for L-arabinonate {ECO:0000269|PubMed:27102126};
CC KM=5.2 mM for D-galactonate {ECO:0000269|PubMed:27102126};
CC KM=5.8 mM for D-fuconate {ECO:0000269|PubMed:27102126};
CC Note=kcat is 1406 min(-1) with D-xylonate as substrate. kcat is 2626
CC min(-1) with D-gluconate as substrate. kcat is 46 min(-1) with L-
CC arabinonate as substrate. kcat is 218 min(-1) with D-galactonate as
CC substrate. kcat is 196 min(-1) with D-fuconate as substrate.
CC {ECO:0000269|PubMed:27102126};
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:27102126};
CC -!- PATHWAY: Carbohydrate metabolism; D-xylose degradation.
CC {ECO:0000269|PubMed:17172333}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:27102126,
CC ECO:0000269|PubMed:29339766}.
CC -!- DISRUPTION PHENOTYPE: Deletion mutant cannot grow with D-xylose as the
CC sole carbon source. {ECO:0000269|PubMed:17172333}.
CC -!- SIMILARITY: Belongs to the IlvD/Edd family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE005673; AAK22804.1; -; Genomic_DNA.
DR PIR; H87350; H87350.
DR RefSeq; NP_419636.1; NC_002696.2.
DR PDB; 5OYN; X-ray; 2.70 A; A/B/C/D=6-595.
DR PDBsum; 5OYN; -.
DR AlphaFoldDB; Q9A9Z2; -.
DR SMR; Q9A9Z2; -.
DR STRING; 190650.CC_0819; -.
DR EnsemblBacteria; AAK22804; AAK22804; CC_0819.
DR KEGG; ccr:CC_0819; -.
DR PATRIC; fig|190650.5.peg.832; -.
DR eggNOG; COG0129; Bacteria.
DR HOGENOM; CLU_014271_3_1_5; -.
DR OMA; FDFAIMK; -.
DR BioCyc; CAULO:CC0819-MON; -.
DR BRENDA; 4.2.1.82; 1218.
DR UniPathway; UPA00810; -.
DR Proteomes; UP000001816; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0047929; F:gluconate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050401; F:xylonate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0019752; P:carboxylic acid metabolic process; IEA:UniProt.
DR GO; GO:0042843; P:D-xylose catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.50.30.80; -; 1.
DR InterPro; IPR042096; Dihydro-acid_dehy_C.
DR InterPro; IPR000581; DiOHA_6PGluconate_deHydtase.
DR InterPro; IPR020558; DiOHA_6PGluconate_deHydtase_CS.
DR InterPro; IPR037237; IlvD/EDD_N.
DR Pfam; PF00920; ILVD_EDD; 1.
DR SUPFAM; SSF143975; SSF143975; 1.
DR PROSITE; PS00886; ILVD_EDD_1; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Carbohydrate metabolism; Iron; Iron-sulfur; Lyase;
KW Magnesium; Metal-binding; Reference proteome; Xylose metabolism.
FT CHAIN 1..595
FT /note="D-xylonate dehydratase"
FT /id="PRO_0000448800"
FT BINDING 64
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:29339766"
FT BINDING 96
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:29339766"
FT BINDING 132
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:29339766"
FT BINDING 133
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:29339766"
FT BINDING 205
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:29339766"
FT BINDING 467
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:29339766"
FT MUTAGEN 64
FT /note="C->S: Strong decrease in activity. Does not bind
FT iron-sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 132
FT /note="C->S: Almost loss of activity. Does not bind iron-
FT sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 205
FT /note="C->S: Strong decrease in activity. Does not bind
FT iron-sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT MUTAGEN 450
FT /note="C->S: Slight decrease in activity. Does not affect
FT binding of iron-sulfur cluster."
FT /evidence="ECO:0000269|PubMed:27102126"
FT HELIX 16..19
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 25..34
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 35..38
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 42..46
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 51..56
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 63..67
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 68..82
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 106..120
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 125..130
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 135..146
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 172..182
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 188..197
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 210..220
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 226..230
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 236..254
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 259..262
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 265..277
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 284..294
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 301..307
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 317..319
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 320..322
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 324..330
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 332..342
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 355..357
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 358..362
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 370..372
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 376..378
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 380..383
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 390..393
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 395..399
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 401..403
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 406..412
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 421..430
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 431..438
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 442..444
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 450..456
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 459..463
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 475..479
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 487..492
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 502..507
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 509..511
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 514..516
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 523..527
FT /evidence="ECO:0007829|PDB:5OYN"
FT TURN 528..531
FT /evidence="ECO:0007829|PDB:5OYN"
FT STRAND 532..535
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 539..546
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 559..567
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 571..573
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 578..581
FT /evidence="ECO:0007829|PDB:5OYN"
FT HELIX 586..588
FT /evidence="ECO:0007829|PDB:5OYN"
SQ SEQUENCE 595 AA; 64626 MW; C0F329411CBB089D CRC64;
MRSALSNRTP RRFRSRDWFD NPDHIDMTAL YLERFMNYGI TPEELRSGKP IIGIAQTGSD
ISPCNRIHLD LVQRVRDGIR DAGGIPMEFP VHPIFENCRR PTAALDRNLS YLGLVETLHG
YPIDAVVLTT GCDKTTPAGI MAATTVNIPA IVLSGGPMLD GWHENELVGS GTVIWRSRRK
LAAGEITEEE FIDRAASSAP SAGHCNTMGT ASTMNAVAEA LGLSLTGCAA IPAPYRERGQ
MAYKTGQRIV DLAYDDVKPL DILTKQAFEN AIALVAAAGG STNAQPHIVA MARHAGVEIT
ADDWRAAYDI PLIVNMQPAG KYLGERFHRA GGAPAVLWEL LQQGRLHGDV LTVTGKTMSE
NLQGRETSDR EVIFPYHEPL AEKAGFLVLK GNLFDFAIMK SSVIGEEFRK RYLSQPGQEG
VFEARAIVFD GSDDYHKRIN DPALEIDERC ILVIRGAGPI GWPGSAEVVN MQPPDHLLKK
GIMSLPTLGD GRQSGTADSP SILNASPESA IGGGLSWLRT GDTIRIDLNT GRCDALVDEA
TIAARKQDGI PAVPATMTPW QEIYRAHASQ LDTGGVLEFA VKYQDLAAKL PRHNH
