HADC_CLODI
ID HADC_CLODI Reviewed; 375 AA.
AC Q5U923;
DT 13-APR-2016, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 71.
DE RecName: Full=(R)-2-hydroxyisocaproyl-CoA dehydratase beta subunit {ECO:0000303|PubMed:15654892};
DE EC=4.2.1.157 {ECO:0000269|PubMed:15654892};
GN Name=hadC {ECO:0000303|PubMed:15654892}; Synonyms=fldC_1, hgdB, lcdB;
GN ORFNames=BN1095_530008, BN1096_180049, BN1097_160051, CD630DERM_03980,
GN ERS445050_03309, PCZ31_0397;
OS Clostridioides difficile (Peptoclostridium difficile).
OG Plasmid 2.
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Clostridioides.
OX NCBI_TaxID=1496;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION,
RP COFACTOR, SUBUNIT, AND REACTION MECHANISM.
RC STRAIN=DSMZ 1296;
RX PubMed=15654892; DOI=10.1111/j.1742-4658.2004.04498.x;
RA Kim J., Darley D., Buckel W.;
RT "2-hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium
RT difficile.";
RL FEBS J. 272:550-561(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Monot M.;
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=630Derm;
RA Magalhaes I.L.F., Oliveira U., Santos F.R., Vidigal T.H.D.A.,
RA Brescovit A.D., Santos A.J.;
RL Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC 13307;
RG Pathogen Informatics;
RL Submitted (MAR-2015) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Z31;
RA Pereira F.L., Oliveira Junior C.A., Silva R.O.S., Dorela F.A.,
RA Carvalho A.F., Almeida G.M.F., Leal C.A.G., Lobato F.C.F.,
RA Figueiredo H.C.P.;
RL Submitted (NOV-2015) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (4FE-4S)
RP AND SUBSTRATE ANALOG, FUNCTION, COFACTOR, SUBUNIT, AND REACTION MECHANISM.
RC PLASMID=2;
RX PubMed=21366233; DOI=10.1021/ja1076537;
RA Knauer S.H., Buckel W., Dobbek H.;
RT "Structural basis for reductive radical formation and electron recycling in
RT (R)-2-hydroxyisocaproyl-CoA dehydratase.";
RL J. Am. Chem. Soc. 133:4342-4347(2011).
CC -!- FUNCTION: Involved in the reductive branch of L-leucine fermentation.
CC Catalyzes the irreversible beta/alpha-elimination of water from (R)-2-
CC hydroxyisocaproyl-CoA to yield isocaprenoyl-CoA. This beta/alpha-
CC dehydration depends on the reductive formation of ketyl radicals on the
CC substrate generated by injection of a single electron from the ATP-
CC dependent activator protein HadI. The enzyme is specific for the R-
CC isomer. {ECO:0000269|PubMed:15654892, ECO:0000269|PubMed:21366233}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-2-hydroxy-4-methylpentanoyl-CoA = 4-methylpent-2-enoyl-CoA
CC + H2O; Xref=Rhea:RHEA:46924, ChEBI:CHEBI:15377, ChEBI:CHEBI:87119,
CC ChEBI:CHEBI:87120; EC=4.2.1.157;
CC Evidence={ECO:0000269|PubMed:15654892};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:15654892, ECO:0000269|PubMed:21366233};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000269|PubMed:15654892,
CC ECO:0000269|PubMed:21366233};
CC -!- ACTIVITY REGULATION: Activated by HadI. {ECO:0000269|PubMed:15654892}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.05 mM for (R)-2-hydroxyisocaproyl-CoA
CC {ECO:0000269|PubMed:15654892};
CC -!- SUBUNIT: Part of the heterodimeric complex HadBC composed of (R)-2-
CC hydroxyisocaproyl-CoA dehydratase alpha (HadB) and beta (HadC) subunit.
CC {ECO:0000269|PubMed:15654892, ECO:0000269|PubMed:21366233}.
CC -!- SIMILARITY: Belongs to the FldB/FldC dehydratase alpha/beta subunit
CC family. {ECO:0000305}.
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DR EMBL; AY772816; AAV40820.1; -; Genomic_DNA.
DR EMBL; LK932467; CDS83477.1; -; Genomic_DNA.
DR EMBL; LK932350; CDS83581.1; -; Genomic_DNA.
DR EMBL; LK933216; CDT50834.1; -; Genomic_DNA.
DR EMBL; LN614756; CEJ96916.1; -; Genomic_DNA.
DR EMBL; LN831031; CKH72351.1; -; Genomic_DNA.
DR EMBL; CP013196; ALP02351.1; -; Genomic_DNA.
DR RefSeq; WP_003427763.1; NZ_WBMC01000117.1.
DR PDB; 3O3M; X-ray; 1.82 A; B/D=1-375.
DR PDB; 3O3N; X-ray; 2.30 A; B/D=1-375.
DR PDB; 3O3O; X-ray; 2.00 A; B=1-375.
DR PDBsum; 3O3M; -.
DR PDBsum; 3O3N; -.
DR PDBsum; 3O3O; -.
DR AlphaFoldDB; Q5U923; -.
DR SMR; Q5U923; -.
DR GeneID; 66352923; -.
DR KEGG; pdf:CD630DERM_03980; -.
DR BRENDA; 4.2.1.157; 1473.
DR SABIO-RK; Q5U923; -.
DR EvolutionaryTrace; Q5U923; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0016836; F:hydro-lyase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006551; P:leucine metabolic process; IDA:UniProtKB.
DR InterPro; IPR010327; FldB/FldC_alpha/beta.
DR Pfam; PF06050; HGD-D; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Direct protein sequencing; Iron; Iron-sulfur; Lyase;
KW Metal-binding; Plasmid.
FT CHAIN 1..375
FT /note="(R)-2-hydroxyisocaproyl-CoA dehydratase beta
FT subunit"
FT /id="PRO_0000435663"
FT BINDING 72
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:21366233"
FT BINDING 99
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:21366233"
FT BINDING 325
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:21366233"
FT HELIX 2..13
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 15..26
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 40..45
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 62..65
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 73..84
FT /evidence="ECO:0007829|PDB:3O3M"
FT TURN 85..89
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 100..112
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 118..121
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 130..151
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 157..182
FT /evidence="ECO:0007829|PDB:3O3M"
FT TURN 183..187
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 190..198
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 199..202
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 205..221
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 228..237
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 242..250
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 253..260
FT /evidence="ECO:0007829|PDB:3O3M"
FT TURN 261..263
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 277..287
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 301..311
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 316..322
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 326..340
FT /evidence="ECO:0007829|PDB:3O3M"
FT TURN 341..343
FT /evidence="ECO:0007829|PDB:3O3M"
FT STRAND 346..351
FT /evidence="ECO:0007829|PDB:3O3M"
FT HELIX 359..371
FT /evidence="ECO:0007829|PDB:3O3M"
SQ SEQUENCE 375 AA; 42366 MW; A15A0D5DF02CA872 CRC64;
MEAILSKMKE VVENPNAAVK KYKSETGKKA IGCFPVYCPE EIIHAAGMLP VGIWGGQTEL
DLAKQYFPAF ACSIMQSCLE YGLKGAYDEL SGVIIPGMCD TLICLGQNWK SAVPHIKYIS
LVHPQNRKLE AGVKYLISEY KGVKRELEEI CGYEIEEAKI HESIEVYNEH RKTMRDFVEV
AYKHSNTIKP SIRSLVIKSG FFMRKEEHTE LVKDLIAKLN AMPEEVCSGK KVLLTGILAD
SKDILDILED NNISVVADDL AQETRQFRTD VPAGDDALER LARQWSNIEG CSLAYDPKKK
RGSLIVDEVK KKDIDGVIFC MMKFCDPEEY DYPLVRKDIE DSGIPTLYVE IDQQTQNNEQ
ARTRIQTFAE MMSLA
