GARD_ECOLI
ID GARD_ECOLI Reviewed; 523 AA.
AC P39829; Q2M981;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Galactarate dehydratase (L-threo-forming) {ECO:0000255|HAMAP-Rule:MF_02031, ECO:0000303|PubMed:9772162};
DE Short=GalcD {ECO:0000255|HAMAP-Rule:MF_02031, ECO:0000303|PubMed:9772162};
DE EC=4.2.1.42 {ECO:0000255|HAMAP-Rule:MF_02031, ECO:0000269|PubMed:9772162};
GN Name=garD {ECO:0000255|HAMAP-Rule:MF_02031, ECO:0000303|PubMed:10762278};
GN Synonyms=yhaG; OrderedLocusNames=b3128, JW3097;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 449-523.
RX PubMed=2407727; DOI=10.1128/jb.172.3.1587-1594.1990;
RA Baird L., Georgopoulos C.;
RT "Identification, cloning, and characterization of the Escherichia coli sohA
RT gene, a suppressor of the htrA (degP) null phenotype.";
RL J. Bacteriol. 172:1587-1594(1990).
RN [4]
RP IDENTIFICATION.
RA Rudd K.E.;
RL Unpublished observations (DEC-1994).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RX PubMed=9772162; DOI=10.1021/bi981124f;
RA Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily:
RT characterization of the (D)-glucarate/galactarate catabolic pathway in
RT Escherichia coli.";
RL Biochemistry 37:14369-14375(1998).
RN [6]
RP GENE NAME, AND INDUCTION.
RX PubMed=10762278; DOI=10.1128/jb.182.9.2672-2674.2000;
RA Monterrubio R., Baldoma L., Obradors N., Aguilar J., Badia J.;
RT "A common regulator for the operons encoding the enzymes involved in D-
RT galactarate, D-glucarate, and D-glycerate utilization in Escherichia
RT coli.";
RL J. Bacteriol. 182:2672-2674(2000).
RN [7] {ECO:0007744|PDB:3LAZ}
RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 6-96.
RG Midwest center for structural genomics (MCSG);
RT "The crystal structure of the N-terminal domain of D-galactarate
RT dehydratase from Escherichia coli CFT073.";
RL Submitted (JAN-2010) to the PDB data bank.
RN [8] {ECO:0007744|PDB:6U7L}
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH CALCIUM, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND DOMAIN.
RX PubMed=31811683; DOI=10.1002/pro.3796;
RA Rosas-Lemus M., Minasov G., Shuvalova L., Wawrzak Z., Kiryukhina O.,
RA Mih N., Jaroszewski L., Palsson B., Godzik A., Satchell K.J.F.;
RT "Structure of galactarate dehydratase, a new fold in an enolase involved in
RT bacterial fitness after antibiotic treatment.";
RL Protein Sci. 29:711-722(2020).
CC -!- FUNCTION: Catalyzes the dehydration of galactarate to form 5-dehydro-4-
CC deoxy-D-glucarate (5-KDG). {ECO:0000255|HAMAP-Rule:MF_02031,
CC ECO:0000269|PubMed:31811683, ECO:0000269|PubMed:9772162}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=galactarate = 5-dehydro-4-deoxy-D-glucarate + H2O;
CC Xref=Rhea:RHEA:16005, ChEBI:CHEBI:15377, ChEBI:CHEBI:16537,
CC ChEBI:CHEBI:42819; EC=4.2.1.42; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_02031, ECO:0000269|PubMed:31811683,
CC ECO:0000269|PubMed:9772162};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16006;
CC Evidence={ECO:0000269|PubMed:31811683, ECO:0000269|PubMed:9772162};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:31811683};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=800 uM for galactarate {ECO:0000269|PubMed:9772162};
CC Note=kcat is 22 sec(-1). {ECO:0000269|PubMed:9772162};
CC -!- PATHWAY: Carbohydrate acid metabolism; galactarate degradation; D-
CC glycerate from galactarate: step 1/3. {ECO:0000255|HAMAP-Rule:MF_02031,
CC ECO:0000269|PubMed:9772162}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:31811683}.
CC -!- INDUCTION: Induced by galactarate, D-glucarate and D-glycerate.
CC {ECO:0000269|PubMed:10762278}.
CC -!- DOMAIN: Consists of three domains. The N-terminal SAF domain, which
CC forms a beta-clip fold, is likely involved in the substrate
CC recognition. It is connected by a long unstructured linker to the
CC second domain, which serves as a dimerization interface between two
CC monomers. The C-terminal domain represents the catalytic core of the
CC protein and probably contains the metal binding site.
CC {ECO:0000269|PubMed:31811683}.
CC -!- SIMILARITY: Belongs to the UxaA family. {ECO:0000255|HAMAP-
CC Rule:MF_02031, ECO:0000305}.
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DR EMBL; U18997; AAA57931.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76162.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77175.1; -; Genomic_DNA.
DR EMBL; M30178; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; D65102; D65102.
DR RefSeq; NP_417597.1; NC_000913.3.
DR RefSeq; WP_001273753.1; NZ_CP014272.1.
DR PDB; 3LAZ; X-ray; 1.92 A; A/B=1-96.
DR PDB; 6U7L; X-ray; 2.75 A; A/B/C/D=1-523.
DR PDBsum; 3LAZ; -.
DR PDBsum; 6U7L; -.
DR AlphaFoldDB; P39829; -.
DR SMR; P39829; -.
DR BioGRID; 4259485; 24.
DR BioGRID; 851954; 1.
DR IntAct; P39829; 5.
DR STRING; 511145.b3128; -.
DR jPOST; P39829; -.
DR PaxDb; P39829; -.
DR PRIDE; P39829; -.
DR EnsemblBacteria; AAC76162; AAC76162; b3128.
DR EnsemblBacteria; BAE77175; BAE77175; BAE77175.
DR GeneID; 947641; -.
DR KEGG; ecj:JW3097; -.
DR KEGG; eco:b3128; -.
DR PATRIC; fig|1411691.4.peg.3603; -.
DR EchoBASE; EB2413; -.
DR eggNOG; COG2721; Bacteria.
DR HOGENOM; CLU_029189_0_0_6; -.
DR InParanoid; P39829; -.
DR OMA; DVGWELF; -.
DR PhylomeDB; P39829; -.
DR BioCyc; EcoCyc:GALACTARDEHYDRA-MON; -.
DR BioCyc; MetaCyc:GALACTARDEHYDRA-MON; -.
DR SABIO-RK; P39829; -.
DR UniPathway; UPA00565; UER00629.
DR EvolutionaryTrace; P39829; -.
DR PRO; PR:P39829; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008198; F:ferrous iron binding; IDA:EcoCyc.
DR GO; GO:0008867; F:galactarate dehydratase activity; IDA:EcoCyc.
DR GO; GO:0019698; P:D-galacturonate catabolic process; IBA:GO_Central.
DR GO; GO:0046392; P:galactarate catabolic process; IDA:EcoCyc.
DR CDD; cd11613; SAF_AH_GD; 1.
DR HAMAP; MF_02031; Galactar_dehydrat; 1.
DR InterPro; IPR007392; Gal/Altron_deHydtase_C.
DR InterPro; IPR017654; GarD-like.
DR InterPro; IPR032893; GarD_Enterobacteriaceae.
DR InterPro; IPR013974; SAF.
DR InterPro; IPR044144; UxaA/GarD_SAF.
DR Pfam; PF04295; GD_AH_C; 1.
DR Pfam; PF08666; SAF; 1.
DR SMART; SM00858; SAF; 1.
DR TIGRFAMs; TIGR03248; galactar-dH20; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Iron; Lyase; Metal-binding; Reference proteome.
FT CHAIN 1..523
FT /note="Galactarate dehydratase (L-threo-forming)"
FT /id="PRO_0000172285"
FT HELIX 1..3
FT /evidence="ECO:0007829|PDB:3LAZ"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:3LAZ"
FT STRAND 23..29
FT /evidence="ECO:0007829|PDB:3LAZ"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:3LAZ"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:3LAZ"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:3LAZ"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:3LAZ"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 148..159
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 161..163
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 189..198
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 251..270
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 275..278
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 283..290
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 295..297
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 299..312
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 316..319
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 322..325
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 326..331
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 333..335
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 339..355
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 379..386
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 387..390
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 395..399
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 409..413
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 419..429
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 432..440
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 447..449
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 451..457
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 458..463
FT /evidence="ECO:0007829|PDB:6U7L"
FT TURN 464..467
FT /evidence="ECO:0007829|PDB:6U7L"
FT STRAND 469..471
FT /evidence="ECO:0007829|PDB:6U7L"
FT TURN 473..478
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 482..497
FT /evidence="ECO:0007829|PDB:6U7L"
FT HELIX 504..508
FT /evidence="ECO:0007829|PDB:6U7L"
SQ SEQUENCE 523 AA; 56402 MW; 919BCC8B49411BB0 CRC64;
MANIEIRQET PTAFYIKVHD TDNVAIIVND NGLKAGTRFP DGLELIEHIP QGHKVALLDI
PANGEIIRYG EVIGYAVRAI PRGSWIDESM VVLPEAPPLH TLPLATKVPE PLPPLEGYTF
EGYRNADGSV GTKNLLGITT SVHCVAGVVD YVVKIIERDL LPKYPNVDGV VGLNHLYGCG
VAINAPAAVV PIRTIHNISL NPNFGGEVMV IGLGCEKLQP ERLLTGTDDV QAIPVESASI
VSLQDEKHVG FQSMVEDILQ IAERHLQKLN QRQRETCPAS ELVVGMQCGG SDAFSGVTAN
PAVGYASDLL VRCGATVMFS EVTEVRDAIH LLTPRAVNEE VGKRLLEEME WYDNYLNMGK
TDRSANPSPG NKKGGLANVV EKALGSIAKS GKSAIVEVLS PGQRPTKRGL IYAATPASDF
VCGTQQVASG ITVQVFTTGR GTPYGLMAVP VIKMATRTEL ANRWFDLMDI NAGTIATGEE
TIEEVGWKLF HFILDVASGK KKTFSDQWGL HNQLAVFNPA PVT
