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D-galactonate dehydratase family member PC1_0802 (EC 4.2.1.-) (D-mannonate dehydratase) (EC 4.2.1.8)

 MAND_PECCP              Reviewed;         404 AA.
C6D9S0;
09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
01-SEP-2009, sequence version 1.
07-JUN-2017, entry version 53.
RecName: Full=D-galactonate dehydratase family member PC1_0802;
EC=4.2.1.-;
AltName: Full=D-mannonate dehydratase;
EC=4.2.1.8;
OrderedLocusNames=PC1_0802;
Pectobacterium carotovorum subsp. carotovorum (strain PC1).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Pectobacteriaceae; Pectobacterium.
NCBI_TaxID=561230;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=PC1;
US DOE Joint Genome Institute;
Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H.,
Bruce D., Goodwin L., Pitluck S., Munk A.C., Brettin T., Detter J.C.,
Han C., Tapia R., Larimer F., Land M., Hauser L., Kyrpides N.,
Mikhailova N., Balakrishnan V., Glasner J., Perna N.T.;
"Complete sequence of Pectobacterium carotovorum subsp. carotovorum
PC1.";
Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases.
[2]
X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH MAGNESIUM,
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL
PROPERTIES.
STRAIN=PC1;
PubMed=24697546; DOI=10.1021/bi500264p;
Wichelecki D.J., Balthazor B.M., Chau A.C., Vetting M.W.,
Fedorov A.A., Fedorov E.V., Lukk T., Patskovsky Y.V., Stead M.B.,
Hillerich B.S., Seidel R.D., Almo S.C., Gerlt J.A.;
"Discovery of function in the enolase superfamily: D-mannonate and D-
gluconate dehydratases in the D-mannonate dehydratase subgroup.";
Biochemistry 53:2722-2731(2014).
-!- FUNCTION: Has low D-mannonate dehydratase activity (in vitro),
suggesting that this is not a physiological substrate and that it
has no significant role in D-mannonate degradation in vivo. Has no
detectable activity with a panel of 70 other acid sugars (in
vitro). {ECO:0000269|PubMed:24697546}.
-!- CATALYTIC ACTIVITY: D-mannonate = 2-dehydro-3-deoxy-D-gluconate +
H(2)O. {ECO:0000269|PubMed:24697546}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:24697546};
Note=Binds 1 Mg(2+) ion per subunit.
{ECO:0000269|PubMed:24697546};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
Note=kcat is 0.01 sec(-1) with D-mannonate.
{ECO:0000269|PubMed:24697546};
-!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
enzyme family. GalD subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; CP001657; ACT11856.1; -; Genomic_DNA.
RefSeq; WP_012773497.1; NC_012917.1.
PDB; 4E4F; X-ray; 2.00 A; A/B/C/D=1-404.
PDBsum; 4E4F; -.
ProteinModelPortal; C6D9S0; -.
SMR; C6D9S0; -.
STRING; 561230.PC1_0802; -.
EnsemblBacteria; ACT11856; ACT11856; PC1_0802.
GeneID; 29704933; -.
KEGG; pct:PC1_0802; -.
eggNOG; ENOG4105CXK; Bacteria.
eggNOG; COG4948; LUCA.
HOGENOM; HOG000113758; -.
KO; K08323; -.
OMA; FYEPADA; -.
OrthoDB; POG091H0FES; -.
Proteomes; UP000002736; Chromosome.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0008927; F:mannonate dehydratase activity; IDA:UniProtKB.
GO; GO:0016052; P:carbohydrate catabolic process; IDA:UniProtKB.
GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
Gene3D; 3.20.20.120; -; 1.
Gene3D; 3.30.390.10; -; 1.
InterPro; IPR034589; D-mannonate_dehydratase_like.
InterPro; IPR034390; Enolase-like_superfamily.
InterPro; IPR029065; Enolase_C-like.
InterPro; IPR029017; Enolase_N-like.
InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
InterPro; IPR013342; Mandelate_racemase_C.
InterPro; IPR013341; Mandelate_racemase_N_dom.
PANTHER; PTHR43287:SF6; PTHR43287:SF6; 1.
Pfam; PF13378; MR_MLE_C; 1.
Pfam; PF02746; MR_MLE_N; 1.
SFLD; SFLDG00033; mannonate_dehydratase; 1.
SFLD; SFLDS00001; Enolase; 1.
SMART; SM00922; MR_MLE; 1.
PROSITE; PS00908; MR_MLE_1; 1.
PROSITE; PS00909; MR_MLE_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Lyase; Magnesium; Metal-binding.
CHAIN 1 404 D-galactonate dehydratase family member
PC1_0802.
/FTId=PRO_0000429889.
ACT_SITE 159 159 Proton donor/acceptor. {ECO:0000250}.
ACT_SITE 214 214 Proton donor/acceptor. {ECO:0000250}.
METAL 212 212 Magnesium. {ECO:0000269|PubMed:24697546}.
METAL 238 238 Magnesium. {ECO:0000269|PubMed:24697546}.
METAL 264 264 Magnesium. {ECO:0000269|PubMed:24697546}.
BINDING 37 37 Substrate. {ECO:0000250}.
BINDING 122 122 Substrate. {ECO:0000250}.
BINDING 264 264 Substrate. {ECO:0000250}.
BINDING 285 285 Substrate. {ECO:0000250}.
BINDING 314 314 Substrate. {ECO:0000250}.
BINDING 318 318 Substrate. {ECO:0000250}.
BINDING 341 341 Substrate. {ECO:0000250}.
SITE 316 316 Important for activity and substrate
specificity; Pro is observed in family
members with low D-mannonate dehydratase
activity. {ECO:0000250}.
STRAND 2 11 {ECO:0000244|PDB:4E4F}.
STRAND 13 15 {ECO:0000244|PDB:4E4F}.
STRAND 17 24 {ECO:0000244|PDB:4E4F}.
STRAND 29 33 {ECO:0000244|PDB:4E4F}.
HELIX 40 49 {ECO:0000244|PDB:4E4F}.
HELIX 51 55 {ECO:0000244|PDB:4E4F}.
HELIX 63 73 {ECO:0000244|PDB:4E4F}.
HELIX 80 101 {ECO:0000244|PDB:4E4F}.
HELIX 105 109 {ECO:0000244|PDB:4E4F}.
STRAND 113 123 {ECO:0000244|PDB:4E4F}.
HELIX 128 140 {ECO:0000244|PDB:4E4F}.
STRAND 144 148 {ECO:0000244|PDB:4E4F}.
STRAND 172 177 {ECO:0000244|PDB:4E4F}.
STRAND 180 183 {ECO:0000244|PDB:4E4F}.
HELIX 185 203 {ECO:0000244|PDB:4E4F}.
STRAND 206 212 {ECO:0000244|PDB:4E4F}.
HELIX 219 228 {ECO:0000244|PDB:4E4F}.
HELIX 229 232 {ECO:0000244|PDB:4E4F}.
STRAND 235 238 {ECO:0000244|PDB:4E4F}.
HELIX 246 249 {ECO:0000244|PDB:4E4F}.
HELIX 250 253 {ECO:0000244|PDB:4E4F}.
STRAND 260 262 {ECO:0000244|PDB:4E4F}.
HELIX 269 271 {ECO:0000244|PDB:4E4F}.
HELIX 273 277 {ECO:0000244|PDB:4E4F}.
STRAND 282 284 {ECO:0000244|PDB:4E4F}.
TURN 288 292 {ECO:0000244|PDB:4E4F}.
HELIX 293 305 {ECO:0000244|PDB:4E4F}.
TURN 306 308 {ECO:0000244|PDB:4E4F}.
STRAND 310 313 {ECO:0000244|PDB:4E4F}.
HELIX 321 333 {ECO:0000244|PDB:4E4F}.
STRAND 337 341 {ECO:0000244|PDB:4E4F}.
HELIX 347 352 {ECO:0000244|PDB:4E4F}.
STRAND 358 360 {ECO:0000244|PDB:4E4F}.
STRAND 363 365 {ECO:0000244|PDB:4E4F}.
STRAND 368 371 {ECO:0000244|PDB:4E4F}.
HELIX 378 381 {ECO:0000244|PDB:4E4F}.
STRAND 393 396 {ECO:0000244|PDB:4E4F}.
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


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