ID HACB_METJA Reviewed; 170 AA.
AC Q58667;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 27-MAR-2024, entry version 145.
DE RecName: Full=Methanogen homoaconitase small subunit;
DE Short=HACN;
DE EC=4.2.1.114 {ECO:0000269|PubMed:18765671};
DE AltName: Full=Homoaconitate hydratase;
GN Name=hacB; OrderedLocusNames=MJ1271;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP PUTATIVE FUNCTION AS A HOMOACONITASE, LACK OF FUNCTION AS A ISOPROPYLMALATE
RP ISOMERASE, AND SUBUNIT.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=17449626; DOI=10.1128/jb.00166-07;
RA Drevland R.M., Waheed A., Graham D.E.;
RT "Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in
RT Methanocaldococcus jannaschii.";
RL J. Bacteriol. 189:4391-4400(2007).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=18765671; DOI=10.1074/jbc.m802159200;
RA Drevland R.M., Jia Y., Palmer D.R.J., Graham D.E.;
RT "Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B
RT biosynthesis.";
RL J. Biol. Chem. 283:28888-28896(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, AND MUTAGENESIS OF ARG-26 AND
RP THR-27.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=20170198; DOI=10.1021/bi901766z;
RA Jeyakanthan J., Drevland R.M., Gayathri D.R., Velmurugan D., Shinkai A.,
RA Kuramitsu S., Yokoyama S., Graham D.E.;
RT "Substrate specificity determinants of the methanogen homoaconitase enzyme:
RT structure and function of the small subunit.";
RL Biochemistry 49:2687-2696(2010).
CC -!- FUNCTION: Component of a hydro-lyase with broad substrate specificity
CC for cis-unsaturated tricarboxylic acids. Catalyzes both the reversible
CC dehydration of (R)-homocitrate ((R)-2-hydroxybutane-1,2,4-
CC tricarboxylate) to produce cis-homoaconitate ((Z)-but-1-ene-1,2,4-
CC tricarboxylate), and its hydration to homoisocitrate ((1R,2S)-1-
CC hydroxybutane-1,2,4-tricarboxylate). Is also able to hydrate the
CC analogous longer chain substrates cis-homo(2)-aconitate, cis-homo(3)-
CC aconitate, and even the non-physiological cis-homo(4)-aconitate with
CC similar efficiency. These reactions are part of the biosynthesis
CC pathway of coenzyme B. Can also catalyze the hydration of maleate to
CC (R)-malate, and that of cis-aconitate. Cannot catalyze the hydration of
CC citraconate and the dehydration of (S)-homocitrate, citramalate, 2-
CC isopropylmalate, 3-isopropylmalate, citrate or threo-DL-isocitrate.
CC {ECO:0000269|PubMed:18765671, ECO:0000269|PubMed:20170198}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-homocitrate = (2R,3S)-homoisocitrate;
CC Xref=Rhea:RHEA:32303, ChEBI:CHEBI:15404, ChEBI:CHEBI:58884;
CC EC=4.2.1.114; Evidence={ECO:0000269|PubMed:18765671};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32304;
CC Evidence={ECO:0000305|PubMed:18765671};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-homocitrate = cis-homoaconitate + H2O;
CC Xref=Rhea:RHEA:26101, ChEBI:CHEBI:15377, ChEBI:CHEBI:58174,
CC ChEBI:CHEBI:58884; Evidence={ECO:0000269|PubMed:18765671};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:26102;
CC Evidence={ECO:0000305|PubMed:18765671};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3S)-homoisocitrate = cis-homoaconitate + H2O;
CC Xref=Rhea:RHEA:15485, ChEBI:CHEBI:15377, ChEBI:CHEBI:15404,
CC ChEBI:CHEBI:58174; Evidence={ECO:0000269|PubMed:18765671};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:15487;
CC Evidence={ECO:0000305|PubMed:18765671};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cis-(homo)2aconitate + H2O = (2R,3S)-iso(homo)2citrate;
CC Xref=Rhea:RHEA:68416, ChEBI:CHEBI:15377, ChEBI:CHEBI:72710,
CC ChEBI:CHEBI:72722; EC=4.2.1.114;
CC Evidence={ECO:0000269|PubMed:18765671};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:68417;
CC Evidence={ECO:0000305|PubMed:18765671};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cis-(homo)3aconitate + H2O = (2R,3S)-iso(homo)3citrate;
CC Xref=Rhea:RHEA:68420, ChEBI:CHEBI:15377, ChEBI:CHEBI:72712,
CC ChEBI:CHEBI:177881; EC=4.2.1.114;
CC Evidence={ECO:0000269|PubMed:18765671};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:68421;
CC Evidence={ECO:0000305|PubMed:18765671};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-malate = H2O + maleate; Xref=Rhea:RHEA:23692,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15588, ChEBI:CHEBI:30780;
CC Evidence={ECO:0000269|PubMed:18765671};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cis-aconitate + H2O = D-threo-isocitrate;
CC Xref=Rhea:RHEA:22144, ChEBI:CHEBI:15377, ChEBI:CHEBI:15562,
CC ChEBI:CHEBI:16383; Evidence={ECO:0000269|PubMed:20170198};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=22 uM for cis-homoaconitate (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:18765671};
CC KM=30 uM for cis-homo(2)-aconitate (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:18765671};
CC KM=36 uM for cis-homo(3)-aconitate (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:18765671};
CC KM=175 uM for cis-homo(4)-aconitate (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:18765671};
CC KM=330 uM for maleate (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:18765671};
CC KM=1500 uM for (R)-homocitrate (at 60 degrees Celsius);
CC KM=300 uM for cis-aconitate {ECO:0000269|PubMed:20170198};
CC Vmax=0.68 umol/min/mg enzyme for cis-homoaconitate hydration reaction
CC (at 60 degrees Celsius) {ECO:0000269|PubMed:18765671};
CC Vmax=0.60 umol/min/mg enzyme for cis-homo(2)aconitate hydration
CC reaction (at 60 degrees Celsius) {ECO:0000269|PubMed:18765671};
CC Vmax=2.2 umol/min/mg enzyme for cis-homo(3)aconitate hydration
CC reaction (at 60 degrees Celsius) {ECO:0000269|PubMed:18765671};
CC Vmax=5.1 umol/min/mg enzyme for cis-homo(4)aconitate hydration
CC reaction (at 60 degrees Celsius) {ECO:0000269|PubMed:18765671};
CC Vmax=5.5 umol/min/mg enzyme for maleate hydration reaction (at 60
CC degrees Celsius) {ECO:0000269|PubMed:18765671};
CC Vmax=0.59 umol/min/mg enzyme for (R)-homocitrate dehydration reaction
CC (at 60 degrees Celsius) {ECO:0000269|PubMed:18765671};
CC Note=kcat is 0.75 sec(-1) for cis-aconitate hydration reaction
CC (PubMed:20170198). Kinetic parameters measured using the HacAB
CC complex. {ECO:0000269|PubMed:20170198};
CC pH dependence:
CC Optimum pH is 9. Active from pH 8 to 10.
CC {ECO:0000269|PubMed:18765671};
CC -!- PATHWAY: Organic acid metabolism; 2-oxosuberate biosynthesis.
CC -!- SUBUNIT: Heterotetramer of 2 HacA and 2 HacB proteins. Cannot form a
CC complex with LeuC. {ECO:0000269|PubMed:17449626}.
CC -!- SIMILARITY: Belongs to the LeuD family. LeuD type 2 subfamily.
CC {ECO:0000305}.
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DR EMBL; L77117; AAB99277.1; -; Genomic_DNA.
DR PIR; F64458; F64458.
DR RefSeq; WP_010870784.1; NC_000909.1.
DR PDB; 2PKP; X-ray; 2.10 A; A=1-170.
DR PDBsum; 2PKP; -.
DR AlphaFoldDB; Q58667; -.
DR SMR; Q58667; -.
DR STRING; 243232.MJ_1271; -.
DR PaxDb; 243232-MJ_1271; -.
DR EnsemblBacteria; AAB99277; AAB99277; MJ_1271.
DR GeneID; 1452169; -.
DR KEGG; mja:MJ_1271; -.
DR eggNOG; arCOG02230; Archaea.
DR HOGENOM; CLU_081378_1_1_2; -.
DR InParanoid; Q58667; -.
DR OrthoDB; 6505at2157; -.
DR PhylomeDB; Q58667; -.
DR BioCyc; MetaCyc:MONOMER-2005; -.
DR SABIO-RK; Q58667; -.
DR UniPathway; UPA00919; -.
DR EvolutionaryTrace; Q58667; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:1902494; C:catalytic complex; IMP:CAFA.
DR GO; GO:0003994; F:aconitate hydratase activity; IMP:CAFA.
DR GO; GO:0004409; F:homoaconitate hydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0050075; F:maleate hydratase activity; IEA:RHEA.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:CAFA.
DR GO; GO:0008270; F:zinc ion binding; IDA:CAFA.
DR GO; GO:0019298; P:coenzyme B biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd01577; IPMI_Swivel; 1.
DR Gene3D; 3.20.19.10; Aconitase, domain 4; 1.
DR HAMAP; MF_01032; LeuD_type2; 1.
DR InterPro; IPR015928; Aconitase/3IPM_dehydase_swvl.
DR InterPro; IPR000573; AconitaseA/IPMdHydase_ssu_swvl.
DR InterPro; IPR033940; IPMI_Swivel.
DR InterPro; IPR011827; LeuD_type2/HacB/DmdB.
DR NCBIfam; NF040604; HacB_Meth; 1.
DR NCBIfam; TIGR02087; LEUD_arch; 1.
DR PANTHER; PTHR43345:SF2; 3-ISOPROPYLMALATE DEHYDRATASE SMALL SUBUNIT 1-RELATED; 1.
DR PANTHER; PTHR43345; 3-ISOPROPYLMALATE DEHYDRATASE SMALL SUBUNIT 2-RELATED-RELATED; 1.
DR Pfam; PF00694; Aconitase_C; 1.
DR SUPFAM; SSF52016; LeuD/IlvD-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Reference proteome.
FT CHAIN 1..170
FT /note="Methanogen homoaconitase small subunit"
FT /id="PRO_0000141936"
FT MOTIF 24..27
FT /note="YLRT"
FT SITE 26
FT /note="Critical for substrate specificity"
FT MUTAGEN 26..27
FT /note="RT->VY: Creates a promiscuous enzyme with both HACN
FT and IPMI activities."
FT MUTAGEN 26
FT /note="R->K,V: Allows the recognition of substrates of IPMI
FT enzymes since it becomes able to efficiently catalyze
FT citraconate hydration and 3-isopropylmalate dehydration.
FT Largely decreases substrate affinity for cis-homo(1-3)-
FT aconitate."
FT /evidence="ECO:0000269|PubMed:20170198"
FT MUTAGEN 27
FT /note="T->A: Largely decreases substrate affinity for cis-
FT homo(1-3)-aconitate while slightly increases activity on
FT these substrates, and also decreases substrate affinity for
FT maleate. Gains the ability to hydrate citraconate, an IPMI
FT substrate."
FT /evidence="ECO:0000269|PubMed:20170198"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 16..19
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 22..25
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 30..34
FT /evidence="ECO:0007829|PDB:2PKP"
FT TURN 35..41
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 45..48
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 54..57
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 68..75
FT /evidence="ECO:0007829|PDB:2PKP"
FT TURN 76..78
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 81..85
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 89..97
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 107..109
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:2PKP"
FT TURN 120..123
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 124..127
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:2PKP"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 141..148
FT /evidence="ECO:0007829|PDB:2PKP"
FT HELIX 152..164
FT /evidence="ECO:0007829|PDB:2PKP"
SQ SEQUENCE 170 AA; 18665 MW; 58146C478777ECB7 CRC64;
MIIKGRAHKF GDDVDTDAII PGPYLRTTDP YELASHCMAG IDENFPKKVK EGDVIVAGEN
FGCGSSREQA VIAIKYCGIK AVIAKSFARI FYRNAINVGL IPIIANTDEI KDGDIVEIDL
DKEEIVITNK NKTIKCETPK GLEREILAAG GLVNYLKKRK LIQSKKGVKT
//
