IMAND_VIBBS
ID IMAND_VIBBS Reviewed; 399 AA.
AC A5KUH4;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 10-JUL-2007, sequence version 1.
DT 03-AUG-2022, entry version 58.
DE RecName: Full=D-galactonate dehydratase family member VSWAT3_13707;
GN ORFNames=VSWAT3_13707;
OS Vibrionales bacterium (strain SWAT-3).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales;
OC unclassified Vibrionales.
OX NCBI_TaxID=391574;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SWAT-3;
RA Azam F., Ferriera S., Johnson J., Kravitz S., Beeson K., Sutton G.,
RA Rogers Y.-H., Friedman R., Frazier M., Venter J.C.;
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 2-399 IN COMPLEX WITH MAGNESIUM
RP AND D-ARABINONATE, FUNCTION, SUBUNIT, AND LACK OF D-MANNONATE DEHYDRATASE
RP ACTIVITY.
RC STRAIN=SWAT-3;
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 no detectable activity with D-mannonate and with a panel
CC of 70 other acid sugars (in vitro), in spite of the conservation of the
CC residues that are expected to be important for catalytic activity and
CC cofactor binding. May have evolved a divergent function.
CC {ECO:0000269|PubMed:24697546}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000305|PubMed:24697546}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
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DR EMBL; AAZW01000001; EDK31132.1; -; Genomic_DNA.
DR RefSeq; WP_008216050.1; NZ_AAZW01000001.1.
DR PDB; 3DFH; X-ray; 2.20 A; A/B/C=2-385.
DR PDB; 3R25; X-ray; 1.60 A; A/B/C/D/E/F/G/H=1-399.
DR PDB; 3SBF; X-ray; 1.50 A; A/B/C/D=2-399.
DR PDBsum; 3DFH; -.
DR PDBsum; 3R25; -.
DR PDBsum; 3SBF; -.
DR AlphaFoldDB; A5KUH4; -.
DR SMR; A5KUH4; -.
DR EvolutionaryTrace; A5KUH4; -.
DR Proteomes; UP000004912; Unassembled WGS sequence.
DR GO; GO:0000287; F:magnesium ion binding; 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 SFLD; SFLDG00033; mannonate_dehydratase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Magnesium; Metal-binding.
FT CHAIN 1..399
FT /note="D-galactonate dehydratase family member
FT VSWAT3_13707"
FT /id="PRO_0000429917"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 207
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0007744|PDB:3SBF"
FT BINDING 231
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 257
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0007744|PDB:3SBF"
FT BINDING 257
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 278
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0007744|PDB:3SBF"
FT BINDING 307
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0007744|PDB:3SBF"
FT BINDING 334
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0007744|PDB:3SBF"
FT STRAND 5..14
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 21..28
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 44..53
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 55..59
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 67..76
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 84..105
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 109..113
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 117..131
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 132..144
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 149..155
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:3R25"
FT HELIX 161..163
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 178..196
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 199..205
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 212..222
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:3R25"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 242..246
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 262..270
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 275..277
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 281..284
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 287..300
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:3R25"
FT HELIX 314..326
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 340..345
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 362..366
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 371..375
FT /evidence="ECO:0007829|PDB:3SBF"
FT HELIX 385..387
FT /evidence="ECO:0007829|PDB:3SBF"
FT STRAND 388..390
FT /evidence="ECO:0007829|PDB:3SBF"
SQ SEQUENCE 399 AA; 45153 MW; 1CD1514E2F563701 CRC64;
MKETIISDIH CIITKPDRHN LITVVVETNE GVTGFGCATF QQRPLAVKTM VDEYLKPILI
GKNANNIEDL WQMMMVNAYW RNGPVINNAI SGVDMALWDI KAKLAGMPLH QLFGGKSRDA
IPVYTHATSD TMEGIYDLVE GFLEKGYKHI RCQLGFYGGV PTDLHTTQNP TEGSYYDQDQ
YMDNTLTMFK SLREKYGNQF HILHDVHERL FPNQAIQFAK EVEQYKPYFI EDILPPNQTE
WLDNIRSQSS VSLGLGELFN NPEEWKSLIA NRRIDFIRCH VSQIGGITPA LKLGHLCQNF
GVRIAWHCPP DMTPIGAAVN THLNVHLHNA AIQEHVEYNG NTHKVFPNAA EPINGYLYAS
EIAGIGVEID REAAAEFPVM YRPHEWTQSR LPDGAIHTP
