MAND_NOVAD
ID MAND_NOVAD Reviewed; 402 AA.
AC A4XF23;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2007, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=D-mannonate dehydratase;
DE Short=ManD;
DE EC=4.2.1.8;
DE AltName: Full=RspA homolog;
GN Name=manD; OrderedLocusNames=Saro_3675;
OS Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG
OS 56034 / CIP 105152 / NBRC 16084 / F199).
OG Plasmid pNL2.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=279238;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 /
RC F199; PLASMID=pNL2;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chertkov O., Han C., Thomson S., Schmutz J., Larimer F., Land M.,
RA Kyrpides N., Ivanova N., Fredrickson J., Romine M.F., Richardson P.;
RT "Complete sequence of plasmid pNL2 of Novosphingobium aromaticivorans DSM
RT 12444.";
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH D-MANNONIC ACID AND
RP MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP COFACTOR, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF ARG-147; TYR-159;
RP HIS-212; LYS-271; ARG-283; HIS-312 AND GLU-339.
RC STRAIN=ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 /
RC F199;
RX PubMed=17944491; DOI=10.1021/bi701703w;
RA Rakus J.F., Fedorov A.A., Fedorov E.V., Glasner M.E., Vick J.E.,
RA Babbitt P.C., Almo S.C., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: D-Mannonate
RT dehydratase from Novosphingobium aromaticivorans.";
RL Biochemistry 46:12896-12908(2007).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) IN COMPLEX D-MANNONIC ACID AND
RP MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND MUTAGENESIS OF 161-VAL--GLU-169 AND ALA-314.
RC STRAIN=ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 /
RC F199;
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:17944491, 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; Evidence={ECO:0000269|PubMed:17944491,
CC ECO:0000269|PubMed:24697546};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:17944491, ECO:0000269|PubMed:24697546};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:17944491,
CC ECO:0000269|PubMed:24697546};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 1.3 sec(-1) with D-mannonate.
CC {ECO:0000269|PubMed:17944491, ECO:0000269|PubMed:24697546};
CC -!- PATHWAY: Carbohydrate metabolism; pentose and glucuronate
CC interconversion.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17944491}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. GalD subfamily. {ECO:0000305}.
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DR EMBL; CP000677; ABP64534.1; -; Genomic_DNA.
DR RefSeq; WP_011906920.1; NC_009427.1.
DR PDB; 2QJJ; X-ray; 1.80 A; A/B/C/D=1-402.
DR PDB; 2QJM; X-ray; 2.20 A; A/B/C/D=1-402.
DR PDB; 2QJN; X-ray; 2.00 A; A/B/C/D=1-402.
DR PDB; 4K1W; X-ray; 1.65 A; A/B/C/D=1-402.
DR PDB; 4K8G; X-ray; 1.25 A; A=1-402.
DR PDBsum; 2QJJ; -.
DR PDBsum; 2QJM; -.
DR PDBsum; 2QJN; -.
DR PDBsum; 4K1W; -.
DR PDBsum; 4K8G; -.
DR AlphaFoldDB; A4XF23; -.
DR SMR; A4XF23; -.
DR STRING; 279238.Saro_3675; -.
DR EnsemblBacteria; ABP64534; ABP64534; Saro_3675.
DR KEGG; nar:Saro_3675; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_5; -.
DR OMA; EYMRHTE; -.
DR OrthoDB; 1825548at2; -.
DR UniPathway; UPA00246; -.
DR EvolutionaryTrace; A4XF23; -.
DR Proteomes; UP000009134; Plasmid pNL2.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0008927; F:mannonate dehydratase activity; 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; 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 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; Carbohydrate metabolism; Lyase; Magnesium; Metal-binding;
KW Plasmid; Reference proteome.
FT CHAIN 1..402
FT /note="D-mannonate dehydratase"
FT /id="PRO_0000429873"
FT ACT_SITE 159
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17944491"
FT ACT_SITE 212
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17944491"
FT BINDING 37
FT /ligand="substrate"
FT BINDING 122
FT /ligand="substrate"
FT BINDING 210
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17944491"
FT BINDING 236
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17944491"
FT BINDING 262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17944491"
FT BINDING 262
FT /ligand="substrate"
FT BINDING 283
FT /ligand="substrate"
FT BINDING 312
FT /ligand="substrate"
FT BINDING 316
FT /ligand="substrate"
FT BINDING 339
FT /ligand="substrate"
FT SITE 314
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 MUTAGEN 147
FT /note="R->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 147
FT /note="R->K: Decreases catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 159
FT /note="Y->F: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 161..169
FT /note="VGRGKLYYE->AGAGGAGAG: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:24697546"
FT MUTAGEN 212
FT /note="H->N: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 271
FT /note="K->E: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 283
FT /note="R->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 312
FT /note="H->N: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT MUTAGEN 314
FT /note="A->P: Decreases catalytic activity."
FT /evidence="ECO:0000269|PubMed:24697546"
FT MUTAGEN 339
FT /note="E->Q: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17944491"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 17..27
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 40..49
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 51..55
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 80..101
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 105..109
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 115..127
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 128..140
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 144..150
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:2QJJ"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 183..187
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 190..201
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 203..210
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 217..227
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 233..237
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 244..247
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 248..253
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 271..275
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 280..282
FT /evidence="ECO:0007829|PDB:4K8G"
FT TURN 286..290
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 291..304
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 308..311
FT /evidence="ECO:0007829|PDB:4K1W"
FT HELIX 319..331
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 335..339
FT /evidence="ECO:0007829|PDB:4K1W"
FT HELIX 345..350
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 353..358
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 361..364
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 368..372
FT /evidence="ECO:0007829|PDB:4K8G"
FT HELIX 376..379
FT /evidence="ECO:0007829|PDB:4K8G"
FT STRAND 391..394
FT /evidence="ECO:0007829|PDB:4K8G"
SQ SEQUENCE 402 AA; 45244 MW; E22007CDD0538750 CRC64;
MKITAARVII TCPGRNFVTL KIETDQGVYG IGDATLNGRE LSVVAYLQEH VAPCLIGMDP
RRIEDIWQYV YRGAYWRRGP VTMRAIAAVD MALWDIKAKM AGMPLYQLLG GRSRDGIMVY
GHANGSDIAE TVEAVGHYID MGYKAIRAQT GVPGIKDAYG VGRGKLYYEP ADASLPSVTG
WDTRKALNYV PKLFEELRKT YGFDHHLLHD GHHRYTPQEA ANLGKMLEPY QLFWLEDCTP
AENQEAFRLV RQHTVTPLAV GEIFNTIWDA KDLIQNQLID YIRATVVGAG GLTHLRRIAD
LASLYQVRTG CHGATDLSPV TMGCALHFDT WVPNFGIQEY MRHTEETDAV FPHDYWFEKG
ELFVGETPGH GVDIDEELAA KYPYKPAYLP VARLEDGTMW NW
