HMGD_EUBBA
ID HMGD_EUBBA Reviewed; 301 AA.
AC Q0QLF5;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, entry version 66.
DE RecName: Full=2-(hydroxymethyl)glutarate dehydrogenase {ECO:0000303|PubMed:16894175};
DE EC=1.1.1.291;
GN Name=Hgd {ECO:0000312|EMBL:ABC88394.1};
OS Eubacterium barkeri (Clostridium barkeri).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Eubacteriaceae;
OC Eubacterium.
OX NCBI_TaxID=1528;
RN [1] {ECO:0000305, ECO:0000312|EMBL:ABC88394.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, PATHWAY, AND
RP SUBUNIT.
RC STRAIN=ATCC 25849 / DSM 1223 / JCM 1389 / NCIMB 10623 / VKM B-1775 / VPI
RC 5359 {ECO:0000312|EMBL:ABC88394.1};
RX PubMed=16894175; DOI=10.1073/pnas.0601635103;
RA Alhapel A., Darley D.J., Wagener N., Eckel E., Elsner N., Pierik A.J.;
RT "Molecular and functional analysis of nicotinate catabolism in Eubacterium
RT barkeri.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:12341-12346(2006).
RN [2] {ECO:0000305}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=18680749; DOI=10.1016/j.jmb.2008.07.050;
RA Reitz S., Alhapel A., Essen L.O., Pierik A.J.;
RT "Structural and kinetic properties of a beta-hydroxyacid dehydrogenase
RT involved in nicotinate fermentation.";
RL J. Mol. Biol. 382:802-811(2008).
CC -!- FUNCTION: Catalyzes the conversion of 2-formylglutarate to (S)-2-
CC hydroxymethylglutarate. Has very low activity with (S)-3-
CC hydroxyisobutyrate. {ECO:0000269|PubMed:18680749}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2-hydroxymethylglutarate + NAD(+) = 2-formylglutarate +
CC H(+) + NADH; Xref=Rhea:RHEA:15505, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:58776,
CC ChEBI:CHEBI:180543; EC=1.1.1.291;
CC Evidence={ECO:0000269|PubMed:16894175, ECO:0000269|PubMed:18680749};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.24 mM for (S)-2-hydroxymethylglutarate
CC {ECO:0000269|PubMed:18680749};
CC KM=0.14 mM for NAD(+) {ECO:0000269|PubMed:18680749};
CC KM=4 mM for (S)-3-hydroxyisobutyrate {ECO:0000269|PubMed:18680749};
CC -!- PATHWAY: Cofactor degradation; nicotinate degradation; propanoate and
CC pyruvate from 6-hydroxynicotinate: step 3/8.
CC {ECO:0000269|PubMed:16894175}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:16894175,
CC ECO:0000269|PubMed:18680749}.
CC -!- SIMILARITY: Belongs to the HIBADH-related family. {ECO:0000305}.
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DR EMBL; DQ310789; ABC88394.1; -; Genomic_DNA.
DR PDB; 3CKY; X-ray; 2.30 A; A/B/C/D=1-301.
DR PDBsum; 3CKY; -.
DR AlphaFoldDB; Q0QLF5; -.
DR SMR; Q0QLF5; -.
DR STRING; 1528.SAMN04488579_11217; -.
DR KEGG; ag:ABC88394; -.
DR BioCyc; MetaCyc:MON-13674; -.
DR SABIO-RK; Q0QLF5; -.
DR UniPathway; UPA01010; UER01014.
DR EvolutionaryTrace; Q0QLF5; -.
DR GO; GO:0043718; F:2-hydroxymethylglutarate dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:1901848; P:nicotinate catabolic process; IDA:UniProtKB.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR002204; 3-OH-isobutyrate_DH-rel_CS.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR006115; 6PGDH_NADP-bd.
DR InterPro; IPR015815; HIBADH-related.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR029154; NADP-bd.
DR Pfam; PF14833; NAD_binding_11; 1.
DR Pfam; PF03446; NAD_binding_2; 1.
DR PIRSF; PIRSF000103; HIBADH; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00895; 3_HYDROXYISOBUT_DH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Oxidoreductase.
FT CHAIN 1..301
FT /note="2-(hydroxymethyl)glutarate dehydrogenase"
FT /id="PRO_0000403974"
FT ACT_SITE 174
FT /evidence="ECO:0000250|UniProtKB:P0ABQ3"
FT BINDING 8..22
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0ABQ3"
FT BINDING 99
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0ABQ3"
FT BINDING 243
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0ABQ3"
FT STRAND 6..10
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 16..25
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 37..44
FT /evidence="ECO:0007829|PDB:3CKY"
FT TURN 45..47
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 54..60
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 62..66
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 71..79
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 84..87
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 102..114
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 118..121
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 127..132
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 136..142
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 144..157
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 158..166
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 169..197
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 202..210
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 217..222
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 223..228
FT /evidence="ECO:0007829|PDB:3CKY"
FT STRAND 233..237
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 238..255
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 260..274
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:3CKY"
FT HELIX 286..293
FT /evidence="ECO:0007829|PDB:3CKY"
SQ SEQUENCE 301 AA; 30873 MW; 00182B7E309EC11D CRC64;
MEKSIKIGFI GLGAMGKPMA INLLKEGVTV YAFDLMEANV AAVVAQGAQA CENNQKVAAA
SDIIFTSLPN AGIVETVMNG PGGVLSACKA GTVIVDMSSV SPSSTLKMAK VAAEKGIDYV
DAPVSGGTKG AEAGTLTIMV GASEAVFEKI QPVLSVIGKD IYHVGDTGAG DAVKIVNNLL
LGCNMASLAE ALVLGVKCGL KPETMQEIIG KSSGRSYAME AKMEKFIMSG DFAGGFAMDL
QHKDLGLALE AGKEGNVPLP MTAMATQIFE GGRAMGLGRE DMSAVIKVWE QMTGVSVSGG
Q
