HGDB_ACIFV
ID HGDB_ACIFV Reviewed; 379 AA.
AC P11570; D2RM66;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 18-MAY-2010, sequence version 3.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=(R)-2-hydroxyglutaryl-CoA dehydratase, subunit beta {ECO:0000303|PubMed:3691501};
DE EC=4.2.1.167 {ECO:0000305|PubMed:3691501, ECO:0000305|PubMed:7398622, ECO:0000305|PubMed:7607244};
DE AltName: Full=(R)-2-hydroxyglutaryl-CoA dehydratase, component D {ECO:0000303|PubMed:3691501};
GN Name=hgdB {ECO:0000303|PubMed:2659350}; OrderedLocusNames=Acfer_1814;
OS Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP
OS 106432 / VR4).
OC Bacteria; Firmicutes; Negativicutes; Acidaminococcales; Acidaminococcaceae;
OC Acidaminococcus.
OX NCBI_TaxID=591001;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-44, AND
RP SUBCELLULAR LOCATION.
RX PubMed=2659350; DOI=10.1111/j.1432-1033.1989.tb14786.x;
RA Dutscho R., Wohlfarth G., Buckel P., Buckel W.;
RT "Cloning and sequencing of the genes of 2-hydoxyglutaryl-CoA dehydratase
RT from Acidaminococcus fermentans.";
RL Eur. J. Biochem. 181:741-746(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4;
RX PubMed=21304687; DOI=10.4056/sigs.1002553;
RA Chang Y.J., Pukall R., Saunders E., Lapidus A., Copeland A., Nolan M.,
RA Glavina Del Rio T., Lucas S., Chen F., Tice H., Cheng J.F., Han C.,
RA Detter J.C., Bruce D., Goodwin L., Pitluck S., Mikhailova N., Liolios K.,
RA Pati A., Ivanova N., Mavromatis K., Chen A., Palaniappan K., Land M.,
RA Hauser L., Jeffries C.D., Brettin T., Rohde M., Goker M., Bristow J.,
RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of Acidaminococcus fermentans type strain
RT (VR4).";
RL Stand. Genomic Sci. 3:1-14(2010).
RN [3]
RP PROTEIN SEQUENCE OF 2-44, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT,
RP AND PATHWAY.
RX PubMed=3691501; DOI=10.1111/j.1432-1033.1987.tb13631.x;
RA Schweiger G., Dutscho R., Buckel W.;
RT "Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus
RT fermentans. An iron-sulfur protein.";
RL Eur. J. Biochem. 169:441-448(1987).
RN [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4;
RX PubMed=7398622; DOI=10.1111/j.1432-1033.1980.tb04590.x;
RA Buckel W.;
RT "The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate.";
RL Eur. J. Biochem. 106:439-447(1980).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4;
RX PubMed=7607244; DOI=10.1111/j.1432-1033.1995.0698h.x;
RA Mueller U., Buckel W.;
RT "Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus
RT fermentans.";
RL Eur. J. Biochem. 230:698-704(1995).
RN [6]
RP COFACTOR.
RX PubMed=11106419; DOI=10.1046/j.1432-1327.2000.01809.x;
RA Hans M., Buckel W., Bill E.;
RT "The iron-sulfur clusters in 2-hydroxyglutaryl-CoA dehydratase from
RT Acidaminococcus fermentans. Biochemical and spectroscopic investigations.";
RL Eur. J. Biochem. 267:7082-7093(2000).
CC -!- FUNCTION: Involved in the fermentation of L-glutamate via the
CC hydroxyglutarate pathway (PubMed:3691501). Catalyzes the reversible
CC syn-elimination of water from (R)-2-hydroxyglutaryl-CoA to yield (E)-
CC glutaconyl-CoA (PubMed:3691501, PubMed:7398622, PubMed:7607244). The
CC dehydration mechanism involves a transient one electron reduction of
CC the thioester from (R)-2-hydroxyglutaryl-CoA, generating a ketyl
CC radical (PubMed:7607244). Prior to (E)-glutaconyl-CoA formation, the
CC ketyl radical is subsequently reoxidized by electron transfer back to
CC the HgdA-HgdB complex (CompD) to avoid change in oxidation state of the
CC substrate (PubMed:7607244). The appropriate redox state of dehydratase
CC HgdA-HgdB complex (CompD) is maintained by HgdC (CompA) via hydrolysis
CC of ATP and ATP-dependent electron transfer (PubMed:7607244). Since the
CC electron is recycled, the dehydratase is able to perform several
CC turnovers with only catalytic amounts of ATP and substoichiometric
CC amounts of HgdC (CompA) (PubMed:7607244). {ECO:0000269|PubMed:3691501,
CC ECO:0000269|PubMed:7398622, ECO:0000269|PubMed:7607244}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-2-hydroxyglutaryl-CoA = (2E)-glutaconyl-CoA + H2O;
CC Xref=Rhea:RHEA:42448, ChEBI:CHEBI:15377, ChEBI:CHEBI:57353,
CC ChEBI:CHEBI:132946; EC=4.2.1.167;
CC Evidence={ECO:0000305|PubMed:3691501, ECO:0000305|PubMed:7398622,
CC ECO:0000305|PubMed:7607244};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:11106419, ECO:0000269|PubMed:3691501,
CC ECO:0000269|PubMed:7607244};
CC Note=Binds 1 [4Fe-4S] cluster per heterodimer.
CC {ECO:0000269|PubMed:11106419, ECO:0000269|PubMed:7607244,
CC ECO:0000305|PubMed:3691501};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:11106419, ECO:0000269|PubMed:7607244};
CC Note=Binds 1 FMN per heterodimer. {ECO:0000269|PubMed:11106419,
CC ECO:0000269|PubMed:7607244};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11106419, ECO:0000269|PubMed:7607244};
CC -!- ACTIVITY REGULATION: Activated by the HgdC. Reversibly inactivated by
CC oxidants such as 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 4-
CC nitrobenzoate, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone
CC (FCCP) and chloramphenicol. Irreversibly inactivated by oxidants such
CC as hydroxylamine and nitrite. {ECO:0000269|PubMed:7607244}.
CC -!- PATHWAY: Amino-acid degradation; L-glutamate degradation via
CC hydroxyglutarate pathway; crotonoyl-CoA from L-glutamate: step 4/5.
CC {ECO:0000305|PubMed:3691501}.
CC -!- SUBUNIT: The (R)-2-hydroxyglutaryl-CoA dehydratase enzyme system is a
CC heterodimer composed of an alpha subunit (HgdA) and a beta subunit
CC (HgdB). {ECO:0000269|PubMed:7607244, ECO:0000305|PubMed:3691501}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:2659350}.
CC -!- SIMILARITY: Belongs to the FldB/FldC dehydratase alpha/beta subunit
CC family. {ECO:0000305}.
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DR EMBL; X14252; CAA32466.1; -; Genomic_DNA.
DR EMBL; CP001859; ADB48168.1; -; Genomic_DNA.
DR PIR; S04478; DWDXBF.
DR RefSeq; WP_012939151.1; NC_013740.1.
DR AlphaFoldDB; P11570; -.
DR SMR; P11570; -.
DR STRING; 591001.Acfer_1814; -.
DR EnsemblBacteria; ADB48168; ADB48168; Acfer_1814.
DR KEGG; afn:Acfer_1814; -.
DR eggNOG; COG1775; Bacteria.
DR HOGENOM; CLU_053697_0_0_9; -.
DR OMA; SYICRIP; -.
DR OrthoDB; 1815612at2; -.
DR BioCyc; MetaCyc:MON-1044; -.
DR BRENDA; 4.2.1.167; 85.
DR UniPathway; UPA00533; UER00687.
DR Proteomes; UP000001902; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0043717; F:2-hydroxyglutaryl-CoA dehydratase activity; IEA:RHEA.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019552; P:glutamate catabolic process via 2-hydroxyglutarate; IEA:UniProtKB-UniPathway.
DR InterPro; IPR010327; FldB/FldC_alpha/beta.
DR Pfam; PF06050; HGD-D; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Cytoplasm; Direct protein sequencing; Flavoprotein; FMN; Iron;
KW Iron-sulfur; Lyase; Magnesium; Metal-binding; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2659350,
FT ECO:0000269|PubMed:3691501"
FT CHAIN 2..379
FT /note="(R)-2-hydroxyglutaryl-CoA dehydratase, subunit beta"
FT /id="PRO_0000083964"
FT CONFLICT 244
FT /note="M -> T (in Ref. 1; CAA32466)"
FT /evidence="ECO:0000305"
FT CONFLICT 283
FT /note="Q -> H (in Ref. 1; CAA32466)"
FT /evidence="ECO:0000305"
FT CONFLICT 313
FT /note="C -> G (in Ref. 1; CAA32466)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 379 AA; 42028 MW; F9B9C0A633AB7809 CRC64;
MAISALIEEF QKVSASPKTM LAKYKAQGKK AIGCLPYYVP EELVYAAGMV PMGVWGCNGK
QEVRSKEYCA SFYCTIAQQS LEMLLDGTLD GLDGIITPVL CDTLRPMSQN FKVAMKDKMP
VIFLAHPQVR QNAAGKQFTY DAYSEVKGHL EEICGHEITN DAILDAIKVY NKSRAARREF
CKLANEHPDL IPASVRATVL RAAYFMLKDE YTEKLEELNK ELAAAPAGKF DGHKVVVSGI
IYNMPGILKA MDDNKLAIAA DDCAYESRSF AVDAPEDLDN GLQALAVQFS KQKNDVLLYD
PEFAKNTRSE HVCNLVKESG AEGLIVFMMQ FCDPEEMEYP DLKKALDAHH IPHVKIGVDQ
MTRDFGQAQT ALEAFAESL
