GALRD_OCEIH
ID GALRD_OCEIH Reviewed; 391 AA.
AC Q8EMJ9;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Galactarate dehydratase (D-threo-forming);
DE Short=GalrD;
DE EC=4.2.1.158 {ECO:0000269|PubMed:19883118};
DE AltName: Full=GalrD-II;
GN OrderedLocusNames=OB2843;
OS Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC
OS 3954 / HTE831).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Oceanobacillus.
OX NCBI_TaxID=221109;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831;
RX PubMed=12235376; DOI=10.1093/nar/gkf526;
RA Takami H., Takaki Y., Uchiyama I.;
RT "Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge
RT and its unexpected adaptive capabilities to extreme environments.";
RL Nucleic Acids Res. 30:3927-3935(2002).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF WILD-TYPE AND MUTANT PHE-90 IN
RP COMPLEXES WITH MAGNESIUM; GALACTARATE AND (2S)-2-HYDROXYBUTANEDIOATE,
RP FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY,
RP COFACTOR, REGIOCHEMISTRY OF THE REACTION, REACTION MECHANISM, ACTIVE SITES,
RP AND MUTAGENESIS OF HIS-45; TYR-90; ARG-162 AND TYR-164.
RC STRAIN=DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831;
RX PubMed=19883118; DOI=10.1021/bi901731c;
RA Rakus J.F., Kalyanaraman C., Fedorov A.A., Fedorov E.V.,
RA Mills-Groninger F.P., Toro R., Bonanno J., Bain K., Sauder J.M.,
RA Burley S.K., Almo S.C., Jacobson M.P., Gerlt J.A.;
RT "Computation-facilitated assignment of the function in the enolase
RT superfamily: a regiochemically distinct galactarate dehydratase from
RT Oceanobacillus iheyensis.";
RL Biochemistry 48:11546-11558(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH PHOSPHATE.
RC STRAIN=DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831;
RG New York SGX Research Center for Structural Genomics (NYSGXRC);
RT "Crystal structure of divergent enolase from Oceanobacillus iheyensis
RT complexed with phosphate.";
RL Submitted (MAR-2009) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the regioselective dehydration of galactarate into
CC 2-keto-D-threo-4,5-dihydroxyadipate ((2S,3R)-dihydroxy-5-
CC oxohexanedioate). Is not active on other acid sugars.
CC {ECO:0000269|PubMed:19883118}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=galactarate = (2S,3R)-dihydroxy-5-oxohexanedioate + H2O;
CC Xref=Rhea:RHEA:45808, ChEBI:CHEBI:15377, ChEBI:CHEBI:16537,
CC ChEBI:CHEBI:78267; EC=4.2.1.158;
CC Evidence={ECO:0000269|PubMed:19883118};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:19883118};
CC Note=Binds 2 magnesium ions per subunit. {ECO:0000269|PubMed:19883118};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=620 uM for galactarate {ECO:0000269|PubMed:19883118};
CC Note=kcat is 6.8 sec(-1).;
CC -!- MISCELLANEOUS: The enzyme product is the enantiomer of the product
CC obtained in the galactarate dehydratase reaction catalyzed by STM3697;
CC the enzymes thus differ in their regiochemistry of dehydration.
CC {ECO:0000305|PubMed:19883118}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; BA000028; BAC14799.1; -; Genomic_DNA.
DR RefSeq; WP_011067240.1; NC_004193.1.
DR PDB; 2OQY; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-391.
DR PDB; 3ES7; X-ray; 1.90 A; A/B=1-391.
DR PDB; 3ES8; X-ray; 2.20 A; A/B/C/D/E/F/G/H=1-391.
DR PDB; 3FYY; X-ray; 1.80 A; A/B=1-391.
DR PDB; 3GD6; X-ray; 1.60 A; A=1-391.
DR PDB; 3HPF; X-ray; 1.80 A; A/B=1-391.
DR PDBsum; 2OQY; -.
DR PDBsum; 3ES7; -.
DR PDBsum; 3ES8; -.
DR PDBsum; 3FYY; -.
DR PDBsum; 3GD6; -.
DR PDBsum; 3HPF; -.
DR AlphaFoldDB; Q8EMJ9; -.
DR SMR; Q8EMJ9; -.
DR STRING; 221109.22778530; -.
DR DNASU; 1017035; -.
DR EnsemblBacteria; BAC14799; BAC14799; BAC14799.
DR KEGG; oih:OB2843; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_705642_0_0_9; -.
DR OMA; PIFRHRF; -.
DR OrthoDB; 951991at2; -.
DR PhylomeDB; Q8EMJ9; -.
DR BioCyc; MetaCyc:MON-19186; -.
DR BRENDA; 4.2.1.158; 4380.
DR EvolutionaryTrace; Q8EMJ9; -.
DR Proteomes; UP000000822; Chromosome.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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; IPR033977; Galactarate_dehydratase_2.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR034593; Mandelate_racemase_DgoD-like.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR PANTHER; PTHR48080; PTHR48080; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00162; galactarate_dehydratase_2; 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..391
FT /note="Galactarate dehydratase (D-threo-forming)"
FT /id="PRO_0000429329"
FT ACT_SITE 90
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:19883118"
FT ACT_SITE 164
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:19883118"
FT BINDING 15
FT /ligand="substrate"
FT BINDING 42
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 45
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 89
FT /ligand="substrate"
FT BINDING 193
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 221
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 246
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 296
FT /ligand="substrate"
FT BINDING 297
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 385
FT /ligand="substrate"
FT SITE 162
FT /note="Increases basicity of active site Tyr"
FT MUTAGEN 45
FT /note="H->Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19883118"
FT MUTAGEN 90
FT /note="Y->F: 3550-fold reduction in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:19883118"
FT MUTAGEN 162
FT /note="R->N: 17000-fold reduction in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:19883118"
FT MUTAGEN 164
FT /note="Y->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19883118"
FT STRAND 3..15
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 20..30
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 35..40
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 44..48
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 53..64
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 72..82
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 92..112
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 126..130
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 142..155
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 169..183
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 188..193
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 200..210
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 229..238
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 243..246
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 250..259
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 275..287
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 291..294
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 301..311
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 325..328
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 333..336
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 344..346
FT /evidence="ECO:0007829|PDB:3GD6"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 361..366
FT /evidence="ECO:0007829|PDB:3GD6"
FT HELIX 379..384
FT /evidence="ECO:0007829|PDB:3HPF"
SQ SEQUENCE 391 AA; 44342 MW; 339ADDCAD8EA3FB6 CRC64;
MKITDLELHA VGIPRHTGFV NKHVIVKIHT DEGLTGIGEM SDFSHLPLYS VDLHDLKQGL
LSILLGQNPF DLMKINKELT DNFPETMYYY EKGSFIRNGI DNALHDLCAK YLDISVSDFL
GGRVKEKIKV CYPIFRHRFS EEVESNLDVV RQKLEQGFDV FRLYVGKNLD ADEEFLSRVK
EEFGSRVRIK SYDFSHLLNW KDAHRAIKRL TKYDLGLEMI ESPAPRNDFD GLYQLRLKTD
YPISEHVWSF KQQQEMIKKD AIDIFNISPV FIGGLTSAKK AAYAAEVASK DVVLGTTQEL
SVGTAAMAHL GCSLTNINHT SDPTGPELYV GDVVKNRVTY KDGYLYAPDR SVKGLGIELD
ESLLAKYQVP DLSWDNVTVH QLQDRTADTK S
