ACNA_BACSU
ID ACNA_BACSU Reviewed; 909 AA.
AC P09339; Q45059;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Aconitate hydratase A {ECO:0000303|PubMed:3110133};
DE Short=ACN {ECO:0000303|PubMed:3110133};
DE Short=Aconitase {ECO:0000303|PubMed:3110133};
DE EC=4.2.1.3 {ECO:0000269|PubMed:23354745};
DE AltName: Full=Aconitate/2-methylaconitate hydratase {ECO:0000303|PubMed:28956599};
DE EC=4.2.1.- {ECO:0000269|PubMed:28956599};
DE AltName: Full=Iron-responsive protein-like {ECO:0000305|PubMed:10468622};
DE Short=IRP-like {ECO:0000305|PubMed:10468622};
DE AltName: Full=RNA-binding protein {ECO:0000303|PubMed:10468622};
GN Name=citB; OrderedLocusNames=BSU18000;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8969507; DOI=10.1099/13500872-142-11-3097;
RA Rose M., Entian K.-D.;
RT "New genes in the 170 degrees region of the Bacillus subtilis genome encode
RT DNA gyrase subunits, a thioredoxin, a xylanase and an amino acid
RT transporter.";
RL Microbiology 142:3097-3101(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-141.
RA Wilde R.J.;
RL Thesis (1988), University of Sheffield, United Kingdom.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-45, PROTEIN SEQUENCE OF 2-8,
RP FUNCTION AS AN ACONITASE, COFACTOR, AND SUBUNIT.
RX PubMed=3110133; DOI=10.1128/jb.169.7.3062-3067.1987;
RA Dingman D.W., Sonenshein A.L.;
RT "Purification of aconitase from Bacillus subtilis and correlation of its N-
RT terminal amino acid sequence with the sequence of the citB gene.";
RL J. Bacteriol. 169:3062-3067(1987).
RN [5]
RP SEQUENCE REVISION.
RA Sonenshein A.L.;
RL Submitted (JUL-1987) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9393699; DOI=10.1128/jb.179.23.7351-7359.1997;
RA Craig J.E., Ford M.J., Blaydon D.C., Sonenshein A.L.;
RT "A null mutation in the Bacillus subtilis aconitase gene causes a block in
RT Spo0A-phosphate-dependent gene expression.";
RL J. Bacteriol. 179:7351-7359(1997).
RN [7]
RP FUNCTION AS RNA-BINDING PROTEIN.
RX PubMed=10468622; DOI=10.1073/pnas.96.18.10412;
RA Alen C., Sonenshein A.L.;
RT "Bacillus subtilis aconitase is an RNA-binding protein.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:10412-10417(1999).
RN [8]
RP FUNCTION, AND DOMAIN.
RX PubMed=16923907; DOI=10.1128/jb.00249-06;
RA Serio A.W., Pechter K.B., Sonenshein A.L.;
RT "Bacillus subtilis aconitase is required for efficient late-sporulation
RT gene expression.";
RL J. Bacteriol. 188:6396-6405(2006).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-450 AND ARG-741, AND
RP REACTION MECHANISM.
RX PubMed=23354745; DOI=10.1128/jb.01690-12;
RA Pechter K.B., Meyer F.M., Serio A.W., Stuelke J., Sonenshein A.L.;
RT "Two roles for aconitase in the regulation of tricarboxylic acid branch
RT gene expression in Bacillus subtilis.";
RL J. Bacteriol. 195:1525-1537(2013).
RN [10]
RP INDUCTION.
RX PubMed=23139400; DOI=10.1099/mic.0.063388-0;
RA Mittal M., Pechter K.B., Picossi S., Kim H.J., Kerstein K.O.,
RA Sonenshein A.L.;
RT "Dual role of CcpC protein in regulation of aconitase gene expression in
RT Listeria monocytogenes and Bacillus subtilis.";
RL Microbiology 159:68-76(2013).
RN [11]
RP FUNCTION AS A METHYLACONITATE HYDRATASE, AND CATALYTIC ACTIVITY.
RC STRAIN=168;
RX PubMed=28956599; DOI=10.1021/acs.biochem.7b00778;
RA Reddick J.J., Sirkisoon S., Dahal R.A., Hardesty G., Hage N.E., Booth W.T.,
RA Quattlebaum A.L., Mills S.N., Meadows V.G., Adams S.L.H., Doyle J.S.,
RA Kiel B.E.;
RT "First biochemical characterization of a methylcitric acid cycle from
RT Bacillus subtilis strain 168.";
RL Biochemistry 56:5698-5711(2017).
CC -!- FUNCTION: Involved in both the tricarboxylic acid (TCA) and
CC methylcitric acid cycles (PubMed:28956599). Catalyzes the reversible
CC isomerization of citrate to isocitrate via cis-aconitate
CC (PubMed:3110133, PubMed:23354745). Also catalyzes the rehydration of 2-
CC methyl-cis-aconitate to produce 2-methylisocitrate (PubMed:28956599).
CC The apo form of AcnA functions as a RNA-binding regulatory protein
CC which plays a role in the regulation of citrate concentration and in
CC the sporulation. To prevent the accumulation of excessive levels of
CC citrate, it binds near the 5' end of the citZ mRNA, decreasing its
CC stability and thereby limiting the concentration of citrate synthase in
CC the cell. Aconitase also binds to the gerE transcript late in
CC sporulation and stabilizes it for translation, thereby increasing the
CC rate and level of GerE protein accumulation (PubMed:10468622,
CC PubMed:16923907, PubMed:23354745, PubMed:9393699).
CC {ECO:0000269|PubMed:10468622, ECO:0000269|PubMed:16923907,
CC ECO:0000269|PubMed:23354745, ECO:0000269|PubMed:28956599,
CC ECO:0000269|PubMed:3110133, ECO:0000269|PubMed:9393699}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=citrate = D-threo-isocitrate; Xref=Rhea:RHEA:10336,
CC ChEBI:CHEBI:15562, ChEBI:CHEBI:16947; EC=4.2.1.3;
CC Evidence={ECO:0000269|PubMed:23354745};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-hydroxybutane-1,2,3-tricarboxylate = 2-methyl-cis-aconitate
CC + H2O; Xref=Rhea:RHEA:57500, ChEBI:CHEBI:15377, ChEBI:CHEBI:57872,
CC ChEBI:CHEBI:141790; Evidence={ECO:0000269|PubMed:28956599};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:3110133};
CC Note=Binds 1 [4Fe-4S] cluster per subunit.
CC {ECO:0000269|PubMed:3110133};
CC -!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate
CC from oxaloacetate: step 2/2. {ECO:0000305|PubMed:23354745}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:3110133}.
CC -!- INDUCTION: By citrate via CcpC. When citrate is absent, CcpC binds to
CC the sites near the citB promoter and blocks expression. When citrate is
CC present, it causes a change in the interaction of CcpC with its binding
CC sites, resulting in derepression of citB. When citrate is very
CC abundant, CcpC activates citB expression, presumably reflecting a
CC change in the interaction of CcpC with RNA polymerase. Also induced by
CC decoyinine and nutrient depletion. {ECO:0000269|PubMed:23139400}.
CC -!- DOMAIN: Mutagenesis of different positions (F662L, R741F, Q745E, I810T
CC and V853A) on the C-terminal region of citB gene product shows that
CC even B.subtilis mutant has high aconitase catalytic activity, it is
CC defective in sporulation. The defect is at a late stage of sporulation,
CC specifically affecting expression of sigma-K-dependent genes, many of
CC which are important for spore coat assembly and require transcriptional
CC activation by GerE. It strongly suggests that aconitase RNA binding
CC activity may stabilize gerE mRNA in order to allow efficient GerE
CC synthesis and proper timing of spore coat assembly.
CC {ECO:0000269|PubMed:16923907}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a dramatic increase
CC in the concentration of citrate. This accumulation of citrate prevents
CC sporulation due to chelation by citrate of divalent cations required
CC for proper functioning of the Spo0A-initiated phosphorelay.
CC {ECO:0000269|PubMed:9393699}.
CC -!- MISCELLANEOUS: Whether aconitase is active as an enzyme or an RNA-
CC binding protein is determined by the status of an iron-sulfur (4Fe-4S)
CC cluster that is essential for the catalytic activity of all aconitases.
CC Citrate is both cotransported with iron and a chelator of divalent
CC cations, including iron. If the intracellular citrate level becomes
CC excessive, iron will be sequestered away from iron-containing proteins,
CC including aconitase. Since excess citrate greatly stimulates aconitase
CC synthesis via the positive regulatory effect of CcpC, the cell will
CC gain the ability to metabolize citrate at a higher rate. If so much
CC iron has been sequestered that aconitase loses enzymatic activity, the
CC cell will acquire a high concentration of enzymatically inactive but
CC RNA-binding-competent aconitase molecules. These aconitase proteins can
CC bind to the citZ mRNA and reduce the rate of citrate accumulation by
CC restricting the synthesis of citrate synthase protein.
CC {ECO:0000269|PubMed:10468622, ECO:0000269|PubMed:23354745}.
CC -!- SIMILARITY: Belongs to the aconitase/IPM isomerase family.
CC {ECO:0000305}.
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DR EMBL; Z73234; CAA97599.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13684.1; -; Genomic_DNA.
DR EMBL; M16776; AAA22316.1; -; Genomic_DNA.
DR PIR; G69599; G69599.
DR RefSeq; NP_389683.1; NC_000964.3.
DR RefSeq; WP_003245728.1; NZ_JNCM01000035.1.
DR AlphaFoldDB; P09339; -.
DR SMR; P09339; -.
DR IntAct; P09339; 1.
DR MINT; P09339; -.
DR STRING; 224308.BSU18000; -.
DR jPOST; P09339; -.
DR PaxDb; P09339; -.
DR PRIDE; P09339; -.
DR EnsemblBacteria; CAB13684; CAB13684; BSU_18000.
DR GeneID; 938140; -.
DR KEGG; bsu:BSU18000; -.
DR PATRIC; fig|224308.179.peg.1961; -.
DR eggNOG; COG1048; Bacteria.
DR InParanoid; P09339; -.
DR OMA; NGGIMQY; -.
DR PhylomeDB; P09339; -.
DR BioCyc; BSUB:BSU18000-MON; -.
DR BioCyc; MetaCyc:BSU18000-MON; -.
DR BRENDA; 4.2.1.3; 658.
DR UniPathway; UPA00223; UER00718.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0047456; F:2-methylisocitrate dehydratase activity; ISS:UniProtKB.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0003994; F:aconitate hydratase activity; IDA:UniProtKB.
DR GO; GO:0047780; F:citrate dehydratase activity; IEA:UniProtKB-EC.
DR GO; GO:0030350; F:iron-responsive element binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; IDA:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:0006101; P:citrate metabolic process; IBA:GO_Central.
DR GO; GO:0019679; P:propionate metabolic process, methylcitrate cycle; TAS:UniProtKB.
DR GO; GO:0043937; P:regulation of sporulation; IDA:UniProtKB.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IBA:GO_Central.
DR CDD; cd01580; AcnA_IRP_Swivel; 1.
DR Gene3D; 3.20.19.10; -; 1.
DR Gene3D; 3.30.499.10; -; 2.
DR InterPro; IPR044137; AcnA_IRP_Swivel.
DR InterPro; IPR015931; Acnase/IPM_dHydase_lsu_aba_1/3.
DR InterPro; IPR001030; Acoase/IPM_deHydtase_lsu_aba.
DR InterPro; IPR015928; Aconitase/3IPM_dehydase_swvl.
DR InterPro; IPR006249; Aconitase/IRP2.
DR InterPro; IPR018136; Aconitase_4Fe-4S_BS.
DR InterPro; IPR036008; Aconitase_4Fe-4S_dom.
DR InterPro; IPR000573; AconitaseA/IPMdHydase_ssu_swvl.
DR PANTHER; PTHR11670; PTHR11670; 1.
DR Pfam; PF00330; Aconitase; 1.
DR Pfam; PF00694; Aconitase_C; 1.
DR PRINTS; PR00415; ACONITASE.
DR SUPFAM; SSF53732; SSF53732; 1.
DR TIGRFAMs; TIGR01341; aconitase_1; 1.
DR PROSITE; PS00450; ACONITASE_1; 1.
DR PROSITE; PS01244; ACONITASE_2; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Iron; Iron-sulfur; Lyase; Metal-binding;
KW Reference proteome; RNA-binding; Tricarboxylic acid cycle.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:3110133"
FT CHAIN 2..909
FT /note="Aconitate hydratase A"
FT /id="PRO_0000076655"
FT BINDING 450
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P36683"
FT BINDING 516
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P36683"
FT BINDING 519
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P36683"
FT MUTAGEN 450
FT /note="C->S: Loss of aconitase activity. It is glutamate
FT auxotroph and accumulates citrate. Exhibits overexpression
FT of the citB promoter and accumulates high levels of
FT inactive aconitase."
FT /evidence="ECO:0000269|PubMed:23354745"
FT MUTAGEN 741
FT /note="R->E: Same aconitase activity compared to the wild-
FT type. It is glutamate prototroph and accumulates citrate.
FT Exhibits overexpression of the citB promoter and
FT accumulates high levels of active aconitase."
FT /evidence="ECO:0000269|PubMed:23354745"
FT CONFLICT 43..45
FT /note="SKL -> FEA (in Ref. 4; AAA22316)"
FT /evidence="ECO:0000305"
FT CONFLICT 119
FT /note="G -> V (in Ref. 3; no nucleotide entry)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 909 AA; 99334 MW; 9545E734F2BCF735 CRC64;
MANEQKTAAK DVFQARKTFT TNGKTYHYYS LKALEDSGIG KVSKLPYSIK VLLESVLRQV
DGFVIKKEHV ENLAKWGTAE LKDIDVPFKP SRVILQDFTG VPAVVDLASL RKAMAAVGGD
PDKINPEIPV DLVIDHSVQV DKAGTEDALA VNMDLEFERN AERYKFLSWA KKAFNNYQAV
PPATGIVHQV NLEFLASVVH AIEEDGELVT YPDTLVGTDS HTTMINGIGV LGWGVGGIEA
EAGMLGQPSY FPVPEVIGAK LVGKLPNGTT ATDLALKVTQ VLREKGVVGK FVEFFGPGIA
ELPLADRATI ANMAPEYGAT CGFFPVDEEA LNYLRLTGRD PEHIDVVEAY CRSNGLFYTP
DAEDPQFTDV VEIDLSQIEA NLSGPKRPQD LIPLSAMQET FKKQLVSPAG NQGFGLNAEE
ENKEIKFKLL NGEETVMKTG AIAIAAITSC TNTSNPYVLI GAGLVAKKAV ELGLKVPNYV
KTSLAPGSKV VTGYLVNSGL LPYMKELGFN LVGYGCTTCI GNSGPLSPEI EEAVAKNDLL
ITSVLSGNRN FEGRIHPLVK GNYLASPPLV VAYALAGTVN INLKTDPIGV GKDGQNVYFN
DIWPSMDEIN ALVKQTVTPE LFRKEYETVF DDNKRWNEIE TTDEALYKWD NDSTYIQNPP
FFEEMSVEPG KVEPLKGLRV VGKFGDSVTT DHISPAGAIG KDTPAGKYLQ EKGVSPRDFN
SYGSRRGNHE VMMRGTFANI RIKNQIAPGT EGGFTTYWPT GEVTSIYDAC MKYKEDKTGL
VVLAGKDYGM GSSRDWAAKG TNLLGIRTVI AESFERIHRS NLVFMGVLPL QFKQGENADT
LGLTGKEVIE VDVDETVRPR DLVTVRAINE DGNVTTFEAV VRFDSEVEID YYRHGGILQM
VLREKMKQS
