TARD_BRADU
ID TARD_BRADU Reviewed; 389 AA.
AC Q89FH0;
DT 01-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=D(-)-tartrate dehydratase;
DE EC=4.2.1.81;
GN Name=tarD; OrderedLocusNames=bll6730;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
RN [2]
RP IDENTIFICATION.
RX PubMed=24826896; DOI=10.1371/journal.pone.0097250;
RA Shearer A.G., Altman T., Rhee C.D.;
RT "Finding sequences for over 270 orphan enzymes.";
RL PLoS ONE 9:E97250-E97250(2014).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF MUTANT LYS-184 IN COMPLEX WITH
RP D(-)-TARTRATE AND MAGNESIUM, COFACTOR, ACTIVE SITE, FUNCTION, CATALYTIC
RP ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, AND
RP MUTAGENESIS OF LYS-102; LYS-184 AND HIS-322.
RX PubMed=17144653; DOI=10.1021/bi061688g;
RA Yew W.S., Fedorov A.A., Fedorov E.V., Wood B.M., Almo S.C., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: D-tartrate
RT dehydratase from Bradyrhizobium japonicum.";
RL Biochemistry 45:14598-14608(2006).
CC -!- FUNCTION: Catalyzes the dehydration of D-tartrate to oxaloacetate.
CC {ECO:0000269|PubMed:17144653}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S,S)-tartrate = H2O + oxaloacetate; Xref=Rhea:RHEA:18289,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16452, ChEBI:CHEBI:30927; EC=4.2.1.81;
CC Evidence={ECO:0000269|PubMed:17144653};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:17144653};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:17144653};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.086 mM for D-tartrate {ECO:0000269|PubMed:17144653};
CC Note=kcat is 7.3 sec(-1) for D-tartrate.;
CC -!- SUBUNIT: Homooctamer; tetramer of dimers.
CC {ECO:0000269|PubMed:17144653}.
CC -!- MISCELLANEOUS: Reaction mechanism is a simple extension of the two-step
CC reaction catalyzed by other members of the family: Lys-184 initiates
CC the reaction by abstraction of the alpha-proton to generate a Mg(2+)-
CC stabilized enediolate intermediate, and the vinylogous beta-elimination
CC of the 3-OH group is general acid-catalyzed by the His-322,
CC accomplishing the anti-elimination of water. The replacement of the
CC leaving group by solvent-derived hydrogen is stereo-random, suggesting
CC that the enol tautomer of oxaloacetate is the product
CC (PubMed:17144653). {ECO:0000305|PubMed:17144653}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; BA000040; BAC51995.1; -; Genomic_DNA.
DR RefSeq; NP_773370.1; NC_004463.1.
DR RefSeq; WP_011089469.1; NZ_CP011360.1.
DR PDB; 1TZZ; X-ray; 1.86 A; A/B=1-389.
DR PDB; 2DW6; X-ray; 2.30 A; A/B/C/D=1-389.
DR PDB; 2DW7; X-ray; 2.50 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=1-389.
DR PDBsum; 1TZZ; -.
DR PDBsum; 2DW6; -.
DR PDBsum; 2DW7; -.
DR AlphaFoldDB; Q89FH0; -.
DR SMR; Q89FH0; -.
DR STRING; 224911.27355010; -.
DR EnsemblBacteria; BAC51995; BAC51995; BAC51995.
DR GeneID; 64026490; -.
DR KEGG; bja:bll6730; -.
DR PATRIC; fig|224911.44.peg.6751; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_707555_0_0_5; -.
DR InParanoid; Q89FH0; -.
DR OMA; FQPYGGF; -.
DR PhylomeDB; Q89FH0; -.
DR SABIO-RK; Q89FH0; -.
DR EvolutionaryTrace; Q89FH0; -.
DR PRO; PR:Q89FH0; -.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0047808; F:D(-)-tartrate dehydratase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0051260; P:protein homooligomerization; IDA:UniProtKB.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR034611; D-tartrate_dehydratase.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR034593; Mandelate_racemase_DgoD-like.
DR PANTHER; PTHR48080; PTHR48080; 1.
DR PANTHER; PTHR48080:SF5; PTHR48080:SF5; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR SFLD; SFLDF00118; D-tartrate_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..389
FT /note="D(-)-tartrate dehydratase"
FT /id="PRO_0000430443"
FT ACT_SITE 184
FT /note="acceptor"
FT /evidence="ECO:0000269|PubMed:17144653"
FT ACT_SITE 322
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000269|PubMed:17144653"
FT BINDING 21
FT /ligand="substrate"
FT BINDING 55
FT /ligand="substrate"
FT BINDING 102
FT /ligand="substrate"
FT BINDING 156
FT /ligand="substrate"
FT BINDING 182..184
FT /ligand="substrate"
FT BINDING 182
FT /ligand="substrate"
FT BINDING 213..215
FT /ligand="substrate"
FT BINDING 213
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17144653"
FT BINDING 239
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17144653"
FT BINDING 239
FT /ligand="substrate"
FT BINDING 265
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17144653"
FT BINDING 265
FT /ligand="substrate"
FT BINDING 322
FT /ligand="substrate"
FT BINDING 341..343
FT /ligand="substrate"
FT SITE 55
FT /note="Transition state stabilizer"
FT SITE 182
FT /note="Transition state stabilizer"
FT SITE 292
FT /note="Increases basicity of active site His"
FT SITE 341
FT /note="Transition state stabilizer"
FT MUTAGEN 102
FT /note="K->A,M: Loss of dehydration activity."
FT /evidence="ECO:0000269|PubMed:17144653"
FT MUTAGEN 184
FT /note="K->A: Loss of dehydration activity."
FT /evidence="ECO:0000269|PubMed:17144653"
FT MUTAGEN 184
FT /note="K->R: Reduced dehydration activity."
FT /evidence="ECO:0000269|PubMed:17144653"
FT MUTAGEN 322
FT /note="H->N: Decreased but measurable dehydration
FT activity."
FT /evidence="ECO:0000269|PubMed:17144653"
FT STRAND 5..14
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 30..41
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 43..52
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 61..66
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 68..73
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 90..97
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 98..100
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 108..128
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 132..139
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 147..153
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 163..174
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 179..184
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 190..204
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 205..207
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 209..213
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 220..230
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 236..239
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 247..253
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 254..256
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 261..263
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 270..279
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 293..297
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 299..311
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 326..335
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:1TZZ"
FT TURN 348..350
FT /evidence="ECO:0007829|PDB:1TZZ"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 374..376
FT /evidence="ECO:0007829|PDB:1TZZ"
FT HELIX 378..385
FT /evidence="ECO:0007829|PDB:1TZZ"
SQ SEQUENCE 389 AA; 43058 MW; 0FE177A59AB2F82C CRC64;
MSVRIVDVRE ITKPISSPIR NAYIDFTKMT TSLVAVVTDV VREGKRVVGY GFNSNGRYGQ
GGLIRERFAS RILEADPKKL LNEAGDNLDP DKVWAAMMIN EKPGGHGERS VAVGTIDMAV
WDAVAKIAGK PLFRLLAERH GVKANPRVFV YAAGGYYYPG KGLSMLRGEM RGYLDRGYNV
VKMKIGGAPI EEDRMRIEAV LEEIGKDAQL AVDANGRFNL ETGIAYAKML RDYPLFWYEE
VGDPLDYALQ AALAEFYPGP MATGENLFSH QDARNLLRYG GMRPDRDWLQ FDCALSYGLC
EYQRTLEVLK THGWSPSRCI PHGGHQMSLN IAAGLGLGGN ESYPDLFQPY GGFPDGVRVE
NGHITMPDLP GIGFEGKSDL YKEMKALAE
