HGDC_ACIFV
ID HGDC_ACIFV Reviewed; 260 AA.
AC P11568; D2RM68; Q44042;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=(R)-2-hydroxyglutaryl-CoA dehydratase activating ATPase {ECO:0000305};
DE EC=3.6.1.- {ECO:0000305|PubMed:3691501, ECO:0000305|PubMed:7607244};
DE AltName: Full=(R)-2-hydroxyglutaryl-CoA dehydratase activase {ECO:0000305};
DE AltName: Full=(R)-2-hydroxyglutaryl-CoA dehydratase, component A {ECO:0000303|PubMed:7607244};
DE AltName: Full=ATP-coupled electron transfer protein HgdC {ECO:0000303|PubMed:11243821};
DE AltName: Full=Activator of (R)-2-hydroxyglutaryl-CoA dehydratase {ECO:0000303|PubMed:8365476};
GN Name=hgdC {ECO:0000303|PubMed:8365476}; OrderedLocusNames=Acfer_1816;
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].
RX PubMed=8365476; DOI=10.1016/0014-5793(93)80247-r;
RA Bendrat K., Mueller U., Klees A.-G., Buckel W.;
RT "Identification of the gene encoding the activator of (R)-2-
RT hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans by gene
RT expression in Escherichia coli.";
RL FEBS Lett. 329:329-331(1993).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 129-260.
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 [4]
RP PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT,
RP AND PATHWAY.
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 [5]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4;
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 [6]
RP COFACTOR.
RC STRAIN=ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4;
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).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH ATP ANALOG AND
RP IRON-SULFUR (4FE-4S), COFACTOR, AND SUBUNIT.
RX PubMed=11243821; DOI=10.1006/jmbi.2000.4496;
RA Locher K.P., Hans M., Yeh A.P., Schmid B., Buckel W., Rees D.C.;
RT "Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA
RT dehydratase component A.";
RL J. Mol. Biol. 307:297-308(2001).
CC -!- FUNCTION: Involved in the fermentation of L-glutamate via the
CC hydroxyglutarate pathway. HgdC (CompA) has a very low ATPase activity,
CC whose the role is to activate dehydratase HgdA-HgdB complex and then
CC maintain an appropriate redox state via an ATP-dependent electron
CC transfer. The dehydratase requires only catalytic amounts of ATP and
CC substoichiometric amounts of HgdC (CompA) to be functional.
CC {ECO:0000269|PubMed:7607244, ECO:0000305|PubMed:3691501}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000305|PubMed:3691501, ECO:0000305|PubMed:7607244};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:11106419, ECO:0000269|PubMed:11243821,
CC ECO:0000269|PubMed:7607244};
CC Note=Binds 1 [4Fe-4S] cluster per dimer. {ECO:0000269|PubMed:11106419,
CC ECO:0000269|PubMed:11243821, ECO:0000269|PubMed:7607244};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11106419, ECO:0000269|PubMed:11243821,
CC ECO:0000305|PubMed:7607244};
CC -!- ACTIVITY REGULATION: Inactivated by exposure to air within less than 15
CC minutes. {ECO:0000269|PubMed:3691501}.
CC -!- PATHWAY: Amino-acid degradation; L-glutamate degradation via
CC hydroxyglutarate pathway; crotonoyl-CoA from L-glutamate: step 4/5.
CC {ECO:0000305|PubMed:7607244}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11243821,
CC ECO:0000269|PubMed:3691501, ECO:0000269|PubMed:7607244}.
CC -!- MISCELLANEOUS: HgdC (CompA) seems to require NADH to be functional.
CC {ECO:0000305|PubMed:3691501}.
CC -!- SIMILARITY: Belongs to the HgdC family. {ECO:0000305}.
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DR EMBL; X59645; CAA42196.1; -; Genomic_DNA.
DR EMBL; CP001859; ADB48170.1; -; Genomic_DNA.
DR EMBL; X14252; CAA32464.1; -; Genomic_DNA.
DR PIR; S36105; S36105.
DR RefSeq; WP_012939153.1; NC_013740.1.
DR PDB; 1HUX; X-ray; 3.00 A; A/B=1-260.
DR PDBsum; 1HUX; -.
DR AlphaFoldDB; P11568; -.
DR SMR; P11568; -.
DR STRING; 591001.Acfer_1816; -.
DR EnsemblBacteria; ADB48170; ADB48170; Acfer_1816.
DR KEGG; afn:Acfer_1816; -.
DR eggNOG; COG1924; Bacteria.
DR HOGENOM; CLU_066597_0_0_9; -.
DR OMA; ELSCHAM; -.
DR OrthoDB; 1837697at2; -.
DR BioCyc; MetaCyc:MON-20614; -.
DR BRENDA; 4.2.1.167; 85.
DR BRENDA; 5.6.1.9; 85.
DR UniPathway; UPA00533; UER00687.
DR EvolutionaryTrace; P11568; -.
DR Proteomes; UP000001902; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
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; IPR002731; ATPase_BadF.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR008275; CoA_E_activase.
DR Pfam; PF01869; BcrAD_BadFG; 1.
DR SUPFAM; SSF53067; SSF53067; 1.
DR TIGRFAMs; TIGR00241; CoA_E_activ; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; ATP-binding; Direct protein sequencing; Hydrolase;
KW Iron; Iron-sulfur; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7607244"
FT CHAIN 2..260
FT /note="(R)-2-hydroxyglutaryl-CoA dehydratase activating
FT ATPase"
FT /id="PRO_0000083965"
FT BINDING 12..16
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11243821,
FT ECO:0007744|PDB:1HUX"
FT BINDING 127
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:11243821,
FT ECO:0007744|PDB:1HUX"
FT BINDING 166
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:11243821,
FT ECO:0007744|PDB:1HUX"
FT BINDING 220
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11243821,
FT ECO:0007744|PDB:1HUX"
FT BINDING 243
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:11243821,
FT ECO:0007744|PDB:1HUX"
FT CONFLICT 196
FT /note="A -> P (in Ref. 3; CAA32464)"
FT /evidence="ECO:0000305"
FT CONFLICT 209
FT /note="V -> L (in Ref. 3; CAA32464)"
FT /evidence="ECO:0000305"
FT CONFLICT 214..224
FT /note="MTGGVAQNYGV -> HDRRCSPELWL (in Ref. 3; CAA32464)"
FT /evidence="ECO:0000305"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 12..21
FT /evidence="ECO:0007829|PDB:1HUX"
FT TURN 22..24
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 25..33
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 40..52
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 60..66
FT /evidence="ECO:0007829|PDB:1HUX"
FT TURN 67..75
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 82..93
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 107..114
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 132..142
FT /evidence="ECO:0007829|PDB:1HUX"
FT TURN 146..148
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 149..153
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 167..179
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 184..204
FT /evidence="ECO:0007829|PDB:1HUX"
FT STRAND 210..216
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 217..220
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 222..232
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 240..244
FT /evidence="ECO:0007829|PDB:1HUX"
FT HELIX 245..257
FT /evidence="ECO:0007829|PDB:1HUX"
SQ SEQUENCE 260 AA; 27269 MW; 7E97044DB6E805AC CRC64;
MSIYTLGIDV GSTASKCIIL KDGKEIVAKS LVAVGTGTSG PARSISEVLE NAHMKKEDMA
FTLATGYGRN SLEGIADKQM SELSCHAMGA SFIWPNVHTV IDIGGQDVKV IHVENGTMTN
FQMNDKCAAG TGRFLDVMAN ILEVKVSDLA ELGAKSTKRV AISSTCTVFA ESEVISQLSK
GTDKIDIIAG IHRSVASRVI GLANRVGIVK DVVMTGGVAQ NYGVRGALEE GLGVEIKTSP
LAQYNGALGA ALYAYKKAAK
