DGD_PANAM
ID DGD_PANAM Reviewed; 417 AA.
AC D4GJ14;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 18-MAY-2010, sequence version 1.
DT 03-AUG-2022, entry version 64.
DE RecName: Full=D-galactonate dehydratase family member RspA;
DE EC=4.2.1.-;
DE AltName: Full=D-gluconate dehydratase;
DE EC=4.2.1.39;
DE AltName: Full=Starvation sensing protein RspA homolog;
GN Name=rspA; OrderedLocusNames=PANA_0592;
OS Pantoea ananatis (strain LMG 20103).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Erwiniaceae; Pantoea.
OX NCBI_TaxID=706191;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 20103;
RX PubMed=20348253; DOI=10.1128/jb.00060-10;
RA De Maayer P., Chan W.Y., Venter S.N., Toth I.K., Birch P.R., Joubert F.,
RA Coutinho T.A.;
RT "Genome sequence of Pantoea ananatis LMG20103, the causative agent of
RT Eucalyptus blight and dieback.";
RL J. Bacteriol. 192:2936-2937(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND
RP D-GLUCONATE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=LMG 20103;
RX PubMed=24697546; DOI=10.1021/bi500264p;
RA Wichelecki D.J., Balthazor B.M., Chau A.C., Vetting M.W., Fedorov A.A.,
RA Fedorov E.V., Lukk T., Patskovsky Y.V., Stead M.B., Hillerich B.S.,
RA Seidel R.D., Almo S.C., Gerlt J.A.;
RT "Discovery of function in the enolase superfamily: D-mannonate and D-
RT gluconate dehydratases in the D-mannonate dehydratase subgroup.";
RL Biochemistry 53:2722-2731(2014).
CC -!- FUNCTION: Has low D-gluconate dehydratase activity (in vitro),
CC suggesting that it has no significant role in D-gluconate degradation
CC in vivo. Has no detectable activity with a panel of 70 other acid
CC sugars (in vitro). {ECO:0000269|PubMed:24697546}.
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:24697546};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:24697546};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:24697546};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 0.04 sec(-1) with D-gluconate.
CC {ECO:0000269|PubMed:24697546};
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
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DR EMBL; CP001875; ADD75759.1; -; Genomic_DNA.
DR RefSeq; WP_013024487.1; NC_013956.2.
DR PDB; 3T6C; X-ray; 1.60 A; A/B=1-417.
DR PDBsum; 3T6C; -.
DR AlphaFoldDB; D4GJ14; -.
DR SMR; D4GJ14; -.
DR STRING; 706191.PANA_0592; -.
DR EnsemblBacteria; ADD75759; ADD75759; PANA_0592.
DR GeneID; 57269677; -.
DR KEGG; pam:PANA_0592; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_6; -.
DR OMA; IRCHVST; -.
DR OrthoDB; 1825548at2; -.
DR BioCyc; PANA706191:PANA_RS03060-MON; -.
DR Proteomes; UP000001702; Chromosome.
DR GO; GO:0047929; F:gluconate 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 GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR034589; D-mannonate_dehydratase-like.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
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 PANTHER; PTHR48080:SF6; PTHR48080:SF6; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..417
FT /note="D-galactonate dehydratase family member RspA"
FT /id="PRO_0000429897"
FT ACT_SITE 158
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 225
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 43
FT /ligand="substrate"
FT BINDING 127
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 275
FT /ligand="substrate"
FT BINDING 296
FT /ligand="substrate"
FT BINDING 325
FT /ligand="substrate"
FT BINDING 329
FT /ligand="substrate"
FT BINDING 352
FT /ligand="substrate"
FT SITE 327
FT /note="Important for activity and substrate specificity;
FT Pro is observed in family members with low D-mannonate
FT dehydratase activity"
FT /evidence="ECO:0000250"
FT STRAND 6..14
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 21..30
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 45..53
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 56..60
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 68..77
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 85..106
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 110..113
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 120..128
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 133..145
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 155..158
FT /evidence="ECO:0007829|PDB:3T6C"
FT TURN 166..169
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 196..214
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 216..223
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 230..239
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 241..243
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 254..259
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 260..266
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 271..273
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 280..288
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 299..302
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 305..317
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 327..330
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 332..344
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 358..363
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 369..371
FT /evidence="ECO:0007829|PDB:3T6C"
FT STRAND 374..376
FT /evidence="ECO:0007829|PDB:3T6C"
FT HELIX 389..392
FT /evidence="ECO:0007829|PDB:3T6C"
SQ SEQUENCE 417 AA; 46135 MW; F916F2A92992C610 CRC64;
MSNLFITNVK TILTAPGGID LVVVKIETNE PGLYGLGCAT FTQRIYAVQS AIDEYLAPFL
IGKDPARIED IWQSAAVSGY WRNGPVMNNA LSGIDMALWD IKGKQAGLPV YELLGGKCRD
GIALYVHTDG ADEVEVEDSA RAKMEEGYQY IRCQMGMYGG AGTDDLRLIA NRMVKAKNIQ
PKRSPRTKAP GIYFDPEAYA KSIPRLFDHL RNKLGFSVEL LHDAHERITP INAIHMAKAL
EPYQLFFLED PVAPENTEWL KMLRQQSSTP IAMGELFVNV NEWKPLIDNK LIDYIRCHIS
SIGGITPAKK IAIYSELNGV RTAWHSPGDI SPIGVCANMH LDLSSPNFGI QEYTPMNDAL
REVFPGCPEV DQGYAYVNDK PGLGIDINEA LAAKFPCEGG NPTWTMARTP DGTVWRP
