MAND_PECCP
ID MAND_PECCP Reviewed; 404 AA.
AC C6D9S0;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-SEP-2009, sequence version 1.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=D-galactonate dehydratase family member PC1_0802;
DE EC=4.2.1.-;
DE AltName: Full=D-mannonate dehydratase;
DE EC=4.2.1.8;
GN OrderedLocusNames=PC1_0802;
OS Pectobacterium carotovorum subsp. carotovorum (strain PC1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Pectobacteriaceae; Pectobacterium.
OX NCBI_TaxID=561230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PC1;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D.,
RA Goodwin L., Pitluck S., Munk A.C., Brettin T., Detter J.C., Han C.,
RA Tapia R., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.,
RA Balakrishnan V., Glasner J., Perna N.T.;
RT "Complete sequence of Pectobacterium carotovorum subsp. carotovorum PC1.";
RL Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=PC1;
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-mannonate dehydratase activity (in vitro),
CC suggesting that this is not a physiological substrate and that it has
CC no significant role in D-mannonate degradation in vivo. Has no
CC detectable 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 0.01 sec(-1) with D-mannonate.
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; CP001657; ACT11856.1; -; Genomic_DNA.
DR RefSeq; WP_012773497.1; NC_012917.1.
DR PDB; 4E4F; X-ray; 2.00 A; A/B/C/D=1-404.
DR PDBsum; 4E4F; -.
DR AlphaFoldDB; C6D9S0; -.
DR SMR; C6D9S0; -.
DR STRING; 561230.PC1_0802; -.
DR EnsemblBacteria; ACT11856; ACT11856; PC1_0802.
DR KEGG; pct:PC1_0802; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_6_1_6; -.
DR OMA; EYMRHTE; -.
DR OrthoDB; 1825548at2; -.
DR Proteomes; UP000002736; Chromosome.
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; 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.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Metal-binding.
FT CHAIN 1..404
FT /note="D-galactonate dehydratase family member PC1_0802"
FT /id="PRO_0000429889"
FT ACT_SITE 159
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 214
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 37
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 122
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 212
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 238
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 264
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24697546"
FT BINDING 264
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 285
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 314
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 318
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 341
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 316
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 2..11
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 17..24
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 40..49
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 51..55
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 80..101
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 105..109
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 113..123
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 128..140
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 144..148
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 180..183
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 185..203
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 206..212
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 219..228
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 229..232
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 246..249
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 250..253
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 273..277
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 282..284
FT /evidence="ECO:0007829|PDB:4E4F"
FT TURN 288..292
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 293..305
FT /evidence="ECO:0007829|PDB:4E4F"
FT TURN 306..308
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 310..313
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 321..333
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 337..341
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 347..352
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 368..371
FT /evidence="ECO:0007829|PDB:4E4F"
FT HELIX 378..381
FT /evidence="ECO:0007829|PDB:4E4F"
FT STRAND 393..396
FT /evidence="ECO:0007829|PDB:4E4F"
SQ SEQUENCE 404 AA; 45595 MW; A485AC985FBD0D70 CRC64;
MKIVSAEVFV TCPGRNFVTL KITTDSGLTG LGDATLNGRE LPVASYLNDH VCPQLIGRDA
HQIEDIWQYF YKGAYWRRGP VTMSAISAVD MALWDIKAKA ANMPLYQLLG GASRTGVMVY
CHTTGHSIDE VLDDYAKHRD QGFKAIRVQC GVPGMETTYG MAKGKGLAYE PATKGSLPEE
QLWSTEKYLD FTPKLFEAVR DKFGFNEHLL HDMHHRLTPI EAARFGKSVE DYRLFWMEDP
TPAENQACFR LIRQHTVTPI AVGEVFNSIW DCKQLIEEQL IDYIRTTITH AGGITGMRRI
ADFASLYQVR TGSHGPSDLS PICMAAALHF DLWVPNFGVQ EYMGYSEQML EVFPHSWTFD
NGYMHPGEKP GLGIEFDEKL AAKYPYDPAY LPVARLEDGT LWNW
