HACA_METJA
ID HACA_METJA Reviewed; 420 AA.
AC Q58409;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Methanogen homoaconitase large subunit;
DE Short=HACN;
DE EC=4.2.1.114 {ECO:0000269|PubMed:18765671};
DE AltName: Full=Homoaconitate hydratase;
GN Name=hacA; OrderedLocusNames=MJ1003;
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, COFACTOR, SUBSTRATE SPECIFICITY, AND
RP BIOPHYSICOCHEMICAL 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 FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND KINETIC
RP PARAMETERS.
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 -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01027,
CC ECO:0000269|PubMed:18765671};
CC Note=Binds 1 [4Fe-4S] cluster per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_01027, ECO:0000269|PubMed:18765671};
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 {ECO:0000269|PubMed:18765671};
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 {ECO:0000305|PubMed:18765671}.
CC -!- SUBUNIT: Heterotetramer of 2 HacA and 2 HacB proteins.
CC {ECO:0000269|PubMed:17449626}.
CC -!- MISCELLANEOUS: The heterotetramer that can be formed in vitro between
CC HacA and LeuD cannot catalyze citraconate hydration or the dehydration
CC of 2-isopropylmalate or 3-isopropylmalate.
CC -!- SIMILARITY: Belongs to the aconitase/IPM isomerase family. LeuC type 2
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01027}.
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DR EMBL; L77117; AAB99007.1; -; Genomic_DNA.
DR PIR; B64425; B64425.
DR RefSeq; WP_010870516.1; NC_000909.1.
DR PDB; 4KP2; X-ray; 2.50 A; A/B=1-420.
DR PDBsum; 4KP2; -.
DR AlphaFoldDB; Q58409; -.
DR SMR; Q58409; -.
DR STRING; 243232.MJ_1003; -.
DR PRIDE; Q58409; -.
DR EnsemblBacteria; AAB99007; AAB99007; MJ_1003.
DR GeneID; 1451900; -.
DR KEGG; mja:MJ_1003; -.
DR eggNOG; arCOG01698; Archaea.
DR HOGENOM; CLU_006714_3_4_2; -.
DR InParanoid; Q58409; -.
DR OMA; GIEHCLL; -.
DR OrthoDB; 15714at2157; -.
DR PhylomeDB; Q58409; -.
DR BioCyc; MetaCyc:MON-2003; -.
DR BRENDA; 4.2.1.114; 3260.
DR SABIO-RK; Q58409; -.
DR UniPathway; UPA00919; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0003861; F:3-isopropylmalate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0004409; F:homoaconitate hydratase activity; IEA:RHEA.
DR GO; GO:0052633; F:isocitrate hydro-lyase (cis-aconitate-forming) activity; IEA:RHEA.
DR GO; GO:0050075; F:maleate hydratase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009098; P:leucine biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd01583; IPMI; 1.
DR Gene3D; 3.30.499.10; -; 2.
DR HAMAP; MF_01027; LeuC_type2; 1.
DR InterPro; IPR015931; Acnase/IPM_dHydase_lsu_aba_1/3.
DR InterPro; IPR001030; Acoase/IPM_deHydtase_lsu_aba.
DR InterPro; IPR018136; Aconitase_4Fe-4S_BS.
DR InterPro; IPR036008; Aconitase_4Fe-4S_dom.
DR InterPro; IPR011826; HAcnase/IPMdehydase_lsu_prok.
DR InterPro; IPR006251; Homoacnase/IPMdehydase_lsu.
DR InterPro; IPR033941; IPMI_cat.
DR Pfam; PF00330; Aconitase; 1.
DR PRINTS; PR00415; ACONITASE.
DR SUPFAM; SSF53732; SSF53732; 1.
DR TIGRFAMs; TIGR01343; hacA_fam; 1.
DR TIGRFAMs; TIGR02086; IPMI_arch; 1.
DR PROSITE; PS00450; ACONITASE_1; 1.
DR PROSITE; PS01244; ACONITASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding;
KW Reference proteome.
FT CHAIN 1..420
FT /note="Methanogen homoaconitase large subunit"
FT /id="PRO_0000076868"
FT BINDING 302
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01027"
FT BINDING 362
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01027"
FT BINDING 365
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01027"
FT HELIX 3..12
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 21..25
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:4KP2"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 36..46
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 56..59
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 69..85
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 88..91
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 98..105
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 112..117
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 120..126
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 135..144
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 145..150
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 153..159
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 168..179
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 187..193
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 194..198
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 201..209
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 210..214
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 216..221
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 225..233
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 239..246
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 262..265
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 286..289
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 295..299
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 301..304
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 307..317
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 327..330
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 335..342
FT /evidence="ECO:0007829|PDB:4KP2"
FT TURN 343..345
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 346..353
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 364..367
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 369..371
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 378..384
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 390..392
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 397..400
FT /evidence="ECO:0007829|PDB:4KP2"
FT HELIX 403..412
FT /evidence="ECO:0007829|PDB:4KP2"
FT STRAND 413..415
FT /evidence="ECO:0007829|PDB:4KP2"
SQ SEQUENCE 420 AA; 46063 MW; ABDBAD2E101616B6 CRC64;
MTLVEKILSK KVGYEVCAGD SIEVEVDLAM THDGTTPLAY KALKEMSDSV WNPDKIVVAF
DHNVPPNTVK AAEMQKLALE FVKRFGIKNF HKGGEGICHQ ILAENYVLPN MFVAGGDSHT
CTHGAFGAFA TGFGATDMAY IYATGETWIK VPKTIRVDIV GKNENVSAKD IVLRVCKEIG
RRGATYMAIE YGGEVVKNMD MDGRLTLCNM AIEMGGKTGV IEADEITYDY LKKERGLSDE
DIAKLKKERI TVNRDEANYY KEIEIDITDM EEQVAVPHHP DNVKPISDVE GTEINQVFIG
SCTNGRLSDL REAAKYLKGR EVHKDVKLIV IPASKKVFLQ ALKEGIIDIF VKAGAMICTP
GCGPCLGAHQ GVLAEGEICL STTNRNFKGR MGHINSYIYL ASPKIAAISA VKGYITNKLD
