HMPD_RHILO
ID HMPD_RHILO Reviewed; 234 AA.
AC Q988D0;
DT 20-JUN-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase {ECO:0000303|PubMed:17973403};
DE Short=HMPDdc {ECO:0000303|PubMed:17973403};
DE EC=4.1.1.51 {ECO:0000269|PubMed:17973403};
GN OrderedLocusNames=mlr6791 {ECO:0000312|EMBL:BAB53020.1};
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH MANGANESE ION,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP SUBUNIT, ACTIVE SITE, REACTION MECHANISM, AND PATHWAY.
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=17973403; DOI=10.1021/bi701439j;
RA Mukherjee T., McCulloch K.M., Ealick S.E., Begley T.P.;
RT "Gene identification and structural characterization of the pyridoxal 5'-
RT phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate
RT decarboxylase from mesorhizobium loti MAFF303099.";
RL Biochemistry 46:13606-13615(2007).
CC -!- FUNCTION: Involved in the catabolism of pyridoxal 5-phosphate (Vitamin
CC B6). Catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-
CC dicarboxylate to yield 3-hydroxy-2-methylpyridine-5-carboxylate. The
CC decarboxylation proceeds by an aldolase-like mechanism in which the
CC binding of the substrate frees Glu-73 residue from its interaction with
CC manganese ion replacing it by an interaction with the hydroxyl group
CC from the substrate. Glu-73 residue then provides the proton for the
CC keto-enol tautomerization. The decarboxylation reaction is analogous to
CC the retroaldol reaction except that it does not need a base as the
CC carboxylate is likely to be deprotonated under the reaction conditions.
CC {ECO:0000269|PubMed:17973403}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-hydroxy-6-methylpyridine-3,4-dicarboxylate + H(+) = 3-
CC hydroxy-2-methylpyridine-5-carboxylate + CO2; Xref=Rhea:RHEA:13669,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57528,
CC ChEBI:CHEBI:77620; EC=4.1.1.51;
CC Evidence={ECO:0000269|PubMed:17973403};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:17973403};
CC Note=Binds 1 manganese ion per subunit. {ECO:0000269|PubMed:17973403};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=366 uM for 3-hydroxy-2-methylpyridine-4,5-dicarboxylate
CC {ECO:0000269|PubMed:17973403};
CC Note=kcat is 0.6 sec(-1) for 3-hydroxy-2-methylpyridine-4,5-
CC dicarboxylate as substrate. {ECO:0000269|PubMed:17973403};
CC -!- PATHWAY: Cofactor degradation; B6 vitamer degradation.
CC {ECO:0000305|PubMed:17973403}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17973403}.
CC -!- SIMILARITY: Belongs to the aldolase class II family. {ECO:0000305}.
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DR EMBL; BA000012; BAB53020.1; -; Genomic_DNA.
DR PDB; 2Z7B; X-ray; 1.90 A; A=1-234.
DR PDBsum; 2Z7B; -.
DR AlphaFoldDB; Q988D0; -.
DR SMR; Q988D0; -.
DR STRING; 266835.14026423; -.
DR EnsemblBacteria; BAB53020; BAB53020; BAB53020.
DR KEGG; mlo:mlr6791; -.
DR eggNOG; COG0235; Bacteria.
DR HOGENOM; CLU_006033_2_2_5; -.
DR OMA; NTIHMAG; -.
DR BioCyc; MetaCyc:MON-20512; -.
DR UniPathway; UPA00192; -.
DR EvolutionaryTrace; Q988D0; -.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0047431; F:3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase activity; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0042820; P:vitamin B6 catabolic process; IDA:UniProtKB.
DR Gene3D; 3.40.225.10; -; 1.
DR InterPro; IPR001303; Aldolase_II/adducin_N.
DR InterPro; IPR036409; Aldolase_II/adducin_N_sf.
DR Pfam; PF00596; Aldolase_II; 1.
DR SMART; SM01007; Aldolase_II; 1.
DR SUPFAM; SSF53639; SSF53639; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Manganese; Metal-binding.
FT CHAIN 1..234
FT /note="3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-
FT decarboxylase"
FT /id="PRO_0000444598"
FT ACT_SITE 73
FT /note="Proton acceptor/donor"
FT /evidence="ECO:0000305|PubMed:17973403"
FT BINDING 73
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17973403,
FT ECO:0007744|PDB:2Z7B"
FT BINDING 92
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17973403,
FT ECO:0007744|PDB:2Z7B"
FT BINDING 94
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17973403,
FT ECO:0007744|PDB:2Z7B"
FT BINDING 163
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17973403,
FT ECO:0007744|PDB:2Z7B"
FT HELIX 1..18
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 38..42
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 74..83
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 89..93
FT /evidence="ECO:0007829|PDB:2Z7B"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 99..102
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 113..118
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 128..131
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 142..152
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 155..160
FT /evidence="ECO:0007829|PDB:2Z7B"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:2Z7B"
FT STRAND 164..171
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 172..193
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 203..209
FT /evidence="ECO:0007829|PDB:2Z7B"
FT HELIX 216..230
FT /evidence="ECO:0007829|PDB:2Z7B"
SQ SEQUENCE 234 AA; 25939 MW; 76E7783A748E0F24 CRC64;
MRRKVFEELV TATKILLNEG IMDTFGHISA RDPEDPASFF LAQKLAPSLI TVDDIQRFNL
DGETSDNRPS YLERYIHSEI YKTRPDVQCV LHTHSPAVLP YCFVDTPLRP VTHMGAFIGE
SVPVYEIRDK HGDETDLFGG SPDVCADIAE SLGSQTVVLM ARHGVVNVGK SVREVVFRAF
YLEQEAAALT AGLKIGNVKY LSPGEIKTAG KLVGAQIDRG WNHWSQRLRQ AGLA
