MAND_SPHSS
ID MAND_SPHSS Reviewed; 403 AA.
AC Q1NAJ2;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=D-mannonate dehydratase;
DE Short=ManD;
DE EC=4.2.1.8;
GN ORFNames=SKA58_08619;
OS Sphingomonas sp. (strain SKA58).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=314266;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SKA58;
RA Hagstrom A., Ferriera S., Johnson J., Kravitz S., Halpern A., Remington K.,
RA Beeson K., Tran B., Rogers Y.-H., Friedman R., Venter J.C.;
RL Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=SKA58;
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: Catalyzes the dehydration of D-mannonate. Has no detectable
CC activity with a panel of 70 other acid sugars (in vitro).
CC {ECO:0000269|PubMed:24697546}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O;
CC Xref=Rhea:RHEA:20097, ChEBI:CHEBI:15377, ChEBI:CHEBI:17767,
CC ChEBI:CHEBI:57990; EC=4.2.1.8;
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 2.0 sec(-1) with D-mannonate.
CC {ECO:0000269|PubMed:24697546};
CC -!- PATHWAY: Carbohydrate metabolism; pentose and glucuronate
CC interconversion.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
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DR EMBL; AAQG01000013; EAT08014.1; -; Genomic_DNA.
DR RefSeq; WP_009821493.1; NZ_CH959306.1.
DR PDB; 3THU; X-ray; 1.80 A; A/B/C=1-403.
DR PDBsum; 3THU; -.
DR AlphaFoldDB; Q1NAJ2; -.
DR SMR; Q1NAJ2; -.
DR STRING; 314266.SKA58_08619; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_5; -.
DR UniPathway; UPA00246; -.
DR EvolutionaryTrace; Q1NAJ2; -.
DR Proteomes; UP000005395; Unassembled WGS sequence.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0008927; F:mannonate dehydratase activity; IDA:CACAO.
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; IPR034587; MAND.
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; SFLDF00001; 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; Carbohydrate metabolism; Lyase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..403
FT /note="D-mannonate dehydratase"
FT /id="PRO_0000429874"
FT ACT_SITE 160
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 213
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 38
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 123
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 211
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 237
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 263
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 284
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 313
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 317
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 340
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 315
FT /note="Important for activity and substrate specificity;
FT Ala is observed in family members with high D-mannonate
FT dehydratase activity that have no activity with D-
FT gluconate"
FT /evidence="ECO:0000250"
FT STRAND 3..12
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 18..25
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 41..50
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 52..56
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 64..74
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 81..102
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 106..109
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 114..128
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 129..141
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 145..151
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 179..182
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 184..202
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 204..211
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 218..228
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 234..237
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 245..248
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 249..254
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 272..276
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 281..283
FT /evidence="ECO:0007829|PDB:3THU"
FT TURN 287..291
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 292..304
FT /evidence="ECO:0007829|PDB:3THU"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 320..332
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 346..351
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 367..370
FT /evidence="ECO:0007829|PDB:3THU"
FT HELIX 377..380
FT /evidence="ECO:0007829|PDB:3THU"
FT STRAND 392..395
FT /evidence="ECO:0007829|PDB:3THU"
SQ SEQUENCE 403 AA; 44964 MW; FFFF0B61540FF4C6 CRC64;
MPKIIDAKVI ITCPGRNFVT LKIMTDEGVY GLGDATLNGR ELAVASYLTD HVIPCLIGRD
AHRIEDLWQY LYKGAYWRRG PVTMTAIAAV DMALWDIKGK IAGLPVYQLL GGASREGVMV
YGHANGTTIE DTVKVALDYQ AQGYKAIRLQ CGVPGMASTY GVSKDKYFYE PADADLPTEN
IWNTSKYLRI VPELFKAARE SLGWDVHLLH DIHHRLTPIE AGRLGQDLEP YRPFWLEDAT
PAENQEAFRL IRQHTTAPLA VGEIFNSIWD AKDLIQNQLI DYIRATVVHA GGITHLRRIA
ALADLYQIRT GCHGATDLSP VCMAAALHFD LSVPNFGIQE YMRHMPETDA VFPHAYTFAD
GMMHPGDQPG LGVDIDEDLA AGYEYKRAFL PVNRLEDGTM FNW
