IMAND_VIBH1
ID IMAND_VIBH1 Reviewed; 399 AA.
AC D0X4R4;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 19-JAN-2010, sequence version 1.
DT 03-AUG-2022, entry version 45.
DE RecName: Full=D-galactonate dehydratase family member VME_00770;
GN ORFNames=VME_00770;
OS Vibrio harveyi (strain 1DA3).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=673519;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1DA3;
RX PubMed=19860885; DOI=10.1186/1471-2148-9-258;
RA Thompson C.C., Vicente A.C., Souza R.C., Vasconcelos A.T., Vesth T.,
RA Alves N. Jr., Ussery D.W., Iida T., Thompson F.L.;
RT "Genomic taxonomy of Vibrios.";
RL BMC Evol. Biol. 9:258-258(2009).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH MAGNESIUM; MALEIC
RP ACID AND MALONIC ACID, FUNCTION, SUBUNIT, AND LACK OF D-MANNONATE
RP DEHYDRATASE ACTIVITY.
RC STRAIN=1DA3;
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; ACZC01000001; EEZ90086.1; -; Genomic_DNA.
DR RefSeq; WP_005434298.1; NZ_ACZC01000001.1.
DR PDB; 4GGH; X-ray; 1.90 A; A/B/C/D=1-399.
DR PDB; 4GIR; X-ray; 2.00 A; A/B/C/D=1-399.
DR PDB; 4GIS; X-ray; 1.80 A; A/B=1-399.
DR PDBsum; 4GGH; -.
DR PDBsum; 4GIR; -.
DR PDBsum; 4GIS; -.
DR AlphaFoldDB; D0X4R4; -.
DR SMR; D0X4R4; -.
DR EnsemblBacteria; EEZ90086; EEZ90086; VME_00770.
DR GeneID; 47103153; -.
DR Proteomes; UP000004396; 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 VME_00770"
FT /id="PRO_0000429916"
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:0000250"
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:0000250"
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:0000250"
FT BINDING 307
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0000250"
FT BINDING 334
FT /ligand="D-arabinonate"
FT /ligand_id="ChEBI:CHEBI:16157"
FT /evidence="ECO:0000250"
FT STRAND 5..14
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 21..28
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 44..53
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 55..59
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 67..76
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 84..105
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 109..113
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 117..131
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 132..144
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 148..154
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 178..196
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 199..205
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 212..222
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 236..241
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 242..246
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 275..277
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 281..284
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 287..299
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 314..326
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 340..345
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 362..366
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 371..375
FT /evidence="ECO:0007829|PDB:4GIS"
FT HELIX 385..387
FT /evidence="ECO:0007829|PDB:4GIS"
FT STRAND 388..390
FT /evidence="ECO:0007829|PDB:4GIS"
SQ SEQUENCE 399 AA; 45487 MW; 62EC89E4FE301B87 CRC64;
MNKNTISNIE CVITKPDRHN LITVIVETES GVTGYGCATF QQRPLAVKTM VDEYLKPLLI
GKDANNIEDL WQMMMVNAYW RNGPVINNAI SGVDMALWDI KAKIANMPLH QLFGGKSRDA
IQVYTHATSD TMEGLYEQVD KYLEQGYQHI RCQLGFYGGV PENIQTAQNP TQGSYYDQDQ
YIENTVEMFK NLREKYGKQF HILHDVHERL FPNQAIQFAK QIEQYNPFFI EDILPPSQTE
WLDNIRNQSS VSLALGELFN NPEEWKALII NRRVDFIRCH VSQIGGITPA LKLGHFCESF
GVRIAWHCPP DMTPIGAAVN THLNVHLHNA AIQEHVEYKA NTQRVFPNAA EPINGYLYAS
EIAGIGVEMD REAAQDFPVE YRPHEWTQSR LPDGSIHTP
