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Aconitate hydratase A (ACN) (Aconitase) (EC 4.2.1.3) (Iron-responsive protein-like) (IRP-like) (RNA-binding protein) (Stationary phase enzyme)

 ACNA_ECOLI              Reviewed;         891 AA.
P25516; P78060; P78148;
01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
15-JAN-2008, sequence version 3.
22-NOV-2017, entry version 152.
RecName: Full=Aconitate hydratase A {ECO:0000303|PubMed:10585860};
Short=ACN {ECO:0000303|PubMed:10585860};
Short=Aconitase {ECO:0000303|PubMed:10585860};
EC=4.2.1.3 {ECO:0000269|PubMed:10585860};
AltName: Full=Iron-responsive protein-like {ECO:0000305|PubMed:10589714};
Short=IRP-like {ECO:0000305|PubMed:10589714};
AltName: Full=RNA-binding protein {ECO:0000303|PubMed:10589714};
AltName: Full=Stationary phase enzyme {ECO:0000303|PubMed:10589714};
Name=acnA {ECO:0000303|PubMed:9421904}; Synonyms=acn;
OrderedLocusNames=b1276, JW1268;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=1541275; DOI=10.1111/j.1432-1033.1992.tb16673.x;
Prodromou C., Artymiuk P.J., Guest J.R.;
"The aconitase of Escherichia coli. Nucleotide sequence of the
aconitase gene and amino acid sequence similarity with mitochondrial
aconitases, the iron-responsive-element-binding protein and
isopropylmalate isomerases.";
Eur. J. Biochem. 204:599-609(1992).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9097039; DOI=10.1093/dnares/3.6.363;
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M.,
Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K.,
Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N.,
Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J.,
Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.;
"A 570-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 28.0-40.1 min region on the linkage map.";
DNA Res. 3:363-377(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PROTEIN SEQUENCE OF 2-19, FUNCTION, AND SUBUNIT.
PubMed=1838390; DOI=10.1099/00221287-137-11-2505;
Prodromou C., Haynes M.J., Guest J.R.;
"The aconitase of Escherichia coli: purification of the enzyme and
molecular cloning and map location of the gene (acn).";
J. Gen. Microbiol. 137:2505-2515(1991).
[6]
INDUCTION, AND DISRUPTION PHENOTYPE.
PubMed=8000525; DOI=10.1099/00221287-140-10-2531;
Gruer M.J., Guest J.R.;
"Two genetically-distinct and differentially-regulated aconitases
(AcnA and AcnB) in Escherichia coli.";
Microbiology 140:2531-2541(1994).
[7]
COFACTOR.
PubMed=7588761; DOI=10.1111/j.1432-1033.1995.317_1.x;
Bennett B., Gruer M.J., Guest J.R., Thomson A.J.;
"Spectroscopic characterisation of an aconitase (AcnA) of Escherichia
coli.";
Eur. J. Biochem. 233:317-326(1995).
[8]
DISRUPTION PHENOTYPE.
PubMed=9202458; DOI=10.1099/00221287-143-6-1837;
Gruer M.J., Bradbury A.J., Guest J.R.;
"Construction and properties of aconitase mutants of Escherichia
coli.";
Microbiology 143:1837-1846(1997).
[9]
FUNCTION, AND INDUCTION.
PubMed=9421904; DOI=10.1099/00221287-143-12-3795;
Cunningham L., Gruer M.J., Guest J.R.;
"Transcriptional regulation of the aconitase genes (acnA and acnB) of
Escherichia coli.";
Microbiology 143:3795-3805(1997).
[10]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MAGNETIC
CIRCULAR DICHROISM, EPR SPECTROSCOPY, AND COFACTOR.
PubMed=10585860; DOI=10.1042/bj3440739;
Jordan P.A., Tang Y., Bradbury A.J., Thomson A.J., Guest J.R.;
"Biochemical and spectroscopic characterization of Escherichia coli
aconitases (AcnA and AcnB).";
Biochem. J. 344:739-746(1999).
[11]
FUNCTION AS A RNA-BINDING PROTEIN.
PubMed=10589714; DOI=10.1099/00221287-145-11-3069;
Tang Y., Guest J.R.;
"Direct evidence for mRNA binding and post-transcriptional regulation
by Escherichia coli aconitases.";
Microbiology 145:3069-3079(1999).
[12]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=11932448;
Tang Y., Quail M.A., Artymiuk P.J., Guest J.R., Green J.;
"Escherichia coli aconitases and oxidative stress: post-
transcriptional regulation of sodA expression.";
Microbiology 148:1027-1037(2002).
[13]
INDUCTION.
PubMed=11917098; DOI=10.1073/pnas.032066599;
Masse E., Gottesman S.;
"A small RNA regulates the expression of genes involved in iron
metabolism in Escherichia coli.";
Proc. Natl. Acad. Sci. U.S.A. 99:4620-4625(2002).
[14]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=12486059; DOI=10.1128/JB.185.1.221-230.2003;
Varghese S., Tang Y., Imlay J.A.;
"Contrasting sensitivities of Escherichia coli aconitases A and B to
oxidation and iron depletion.";
J. Bacteriol. 185:221-230(2003).
[15]
INDUCTION.
PubMed=15672380; DOI=10.1002/bit.20389;
Lu C., Albano C.R., Bentley W.E., Rao G.;
"Quantitative and kinetic study of oxidative stress regulons using
green fluorescent protein.";
Biotechnol. Bioeng. 89:574-587(2005).
[16]
INDUCTION.
PubMed=17015655; DOI=10.1128/JB.00508-06;
Weber A., Kogl S.A., Jung K.;
"Time-dependent proteome alterations under osmotic stress during
aerobic and anaerobic growth in Escherichia coli.";
J. Bacteriol. 188:7165-7175(2006).
-!- FUNCTION: Catalyzes the reversible isomerization of citrate to
isocitrate via cis-aconitate. The apo form of AcnA functions as a
RNA-binding regulatory protein which plays a role as a maintenance
or survival enzyme during nutritional or oxidative stress. During
oxidative stress inactive AcnA apo-enzyme without iron sulfur
clusters binds the acnA mRNA 3' UTRs (untranslated regions),
stabilizes acnA mRNA and increases AcnA synthesis, thus mediating
a post-transcriptional positive autoregulatory switch. AcnA also
enhances the stability of the sodA transcript.
{ECO:0000269|PubMed:10585860, ECO:0000269|PubMed:10589714,
ECO:0000269|PubMed:11932448, ECO:0000269|PubMed:12486059,
ECO:0000269|PubMed:1838390, ECO:0000269|PubMed:9421904}.
-!- CATALYTIC ACTIVITY: Citrate = isocitrate.
{ECO:0000269|PubMed:10585860}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000269|PubMed:10585860,
ECO:0000269|PubMed:7588761};
Note=Binds 1 [4Fe-4S] cluster per subunit.
{ECO:0000269|PubMed:10585860, ECO:0000269|PubMed:7588761};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.16 mM for citrate {ECO:0000269|PubMed:10585860};
KM=0.058 mM for cis-aconitate {ECO:0000269|PubMed:10585860};
KM=0.014 mM for isocitrate (using 0.01-0.8 mM substrate)
{ECO:0000269|PubMed:10585860};
KM=1.77 mM for isocitrate (using 0.8-40 mM substrate)
{ECO:0000269|PubMed:10585860};
Vmax=6.13 umol/min/mg enzyme with citrate as substrate
{ECO:0000269|PubMed:10585860};
Vmax=14.5 umol/min/mg enzyme with cis-aconitate as substrate
{ECO:0000269|PubMed:10585860};
Vmax=3.57 umol/min/mg enzyme using 0.01-0.8 mM isocitrate as
substrate {ECO:0000269|PubMed:10585860};
Vmax=14.7 umol/min/mg enzyme using 0.8-40 mM isocitrate as
substrate {ECO:0000269|PubMed:10585860};
pH dependence:
Optimum pH is 7.4. It retains a high specific activity over a
broad pH range. {ECO:0000269|PubMed:10585860};
-!- PATHWAY: Carbohydrate metabolism; tricarboxylic acid cycle;
isocitrate from oxaloacetate: step 2/2. {ECO:0000305}.
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:1838390}.
-!- INDUCTION: Induced upon entry into stationary phase by iron,
oxidative and salt stress under aerobic conditions. AcnA is
subject to CRP-mediated catabolite repression and ArcA-mediated
anaerobic repression. AcnA is negatively regulated by ryhB RNA.
{ECO:0000269|PubMed:11917098, ECO:0000269|PubMed:15672380,
ECO:0000269|PubMed:17015655, ECO:0000269|PubMed:8000525,
ECO:0000269|PubMed:9421904}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene are more sensitive
to peroxide stress. The acnAB double mutant does not grow on
unsupplemented glucose minimal medium and does not respond under
aerobic conditions to glutamate. The acnAB double mutant retains a
low but significant aconitase activity.
{ECO:0000269|PubMed:11932448, ECO:0000269|PubMed:12486059,
ECO:0000269|PubMed:8000525, ECO:0000269|PubMed:9202458}.
-!- MISCELLANEOUS: The AcnA activity over a broad pH range might be a
useful adaptation for specifically expression in the stationary
phase, where the intracellular pH may vary over a wider range.
AcnA is resistant to oxidation in vivo.
{ECO:0000269|PubMed:10585860, ECO:0000269|PubMed:12486059}.
-!- SIMILARITY: Belongs to the aconitase/IPM isomerase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X60293; CAA42834.1; -; Genomic_DNA.
EMBL; U00096; AAC74358.1; -; Genomic_DNA.
EMBL; AP009048; BAA14828.1; -; Genomic_DNA.
PIR; G64875; G64875.
RefSeq; NP_415792.1; NC_000913.3.
RefSeq; WP_000099535.1; NZ_LN832404.1.
ProteinModelPortal; P25516; -.
SMR; P25516; -.
BioGrid; 4260134; 11.
BioGrid; 851065; 1.
DIP; DIP-9043N; -.
IntAct; P25516; 13.
MINT; MINT-1249275; -.
STRING; 316385.ECDH10B_1393; -.
PaxDb; P25516; -.
PRIDE; P25516; -.
EnsemblBacteria; AAC74358; AAC74358; b1276.
EnsemblBacteria; BAA14828; BAA14828; BAA14828.
GeneID; 946724; -.
KEGG; ecj:JW1268; -.
KEGG; eco:b1276; -.
PATRIC; fig|511145.12.peg.1327; -.
EchoBASE; EB1301; -.
EcoGene; EG11325; acnA.
eggNOG; ENOG4107QM5; Bacteria.
eggNOG; COG1048; LUCA.
HOGENOM; HOG000025704; -.
InParanoid; P25516; -.
KO; K01681; -.
PhylomeDB; P25516; -.
BioCyc; EcoCyc:ACONITASE-MONOMER; -.
BioCyc; MetaCyc:ACONITASE-MONOMER; -.
BRENDA; 4.2.1.3; 2026.
SABIO-RK; P25516; -.
UniPathway; UPA00223; UER00718.
PRO; PR:P25516; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoliWiki.
GO; GO:0003994; F:aconitate hydratase activity; IDA:EcoliWiki.
GO; GO:0005506; F:iron ion binding; IMP:EcoliWiki.
GO; GO:0046872; F:metal ion binding; IDA:EcoliWiki.
GO; GO:0003730; F:mRNA 3'-UTR binding; IDA:EcoCyc.
GO; GO:0003729; F:mRNA binding; IDA:EcoliWiki.
GO; GO:0009061; P:anaerobic respiration; IDA:EcoliWiki.
GO; GO:0006097; P:glyoxylate cycle; NAS:EcoliWiki.
GO; GO:0006979; P:response to oxidative stress; IDA:EcoliWiki.
GO; GO:0006099; P:tricarboxylic acid cycle; NAS:EcoliWiki.
Gene3D; 3.20.19.10; -; 1.
Gene3D; 3.30.499.10; -; 2.
Gene3D; 3.40.1060.10; -; 1.
InterPro; IPR015931; Acnase/IPM_dHydase_lsu_aba_1/3.
InterPro; IPR001030; Acoase/IPM_deHydtase_lsu_aba.
InterPro; IPR015928; Aconitase/3IPM_dehydase_swvl.
InterPro; IPR015932; Aconitase/IPMdHydase_lsu_aba_2.
InterPro; IPR006249; Aconitase/IRP2.
InterPro; IPR018136; Aconitase_4Fe-4S_BS.
InterPro; IPR036008; Aconitase_4Fe-4S_dom.
InterPro; IPR000573; AconitaseA/IPMdHydase_ssu_swvl.
PANTHER; PTHR11670; PTHR11670; 1.
Pfam; PF00330; Aconitase; 1.
Pfam; PF00694; Aconitase_C; 1.
PRINTS; PR00415; ACONITASE.
SUPFAM; SSF53732; SSF53732; 1.
TIGRFAMs; TIGR01341; aconitase_1; 1.
PROSITE; PS00450; ACONITASE_1; 1.
PROSITE; PS01244; ACONITASE_2; 1.
1: Evidence at protein level;
4Fe-4S; Complete proteome; Direct protein sequencing; Iron;
Iron-sulfur; Lyase; Metal-binding; Reference proteome; RNA-binding;
Tricarboxylic acid cycle.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:1838390}.
CHAIN 2 891 Aconitate hydratase A.
/FTId=PRO_0000076661.
METAL 435 435 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P36683}.
METAL 501 501 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P36683}.
METAL 504 504 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P36683}.
CONFLICT 522 522 S -> G (in Ref. 1; CAA42834 and 4;
BAA14828). {ECO:0000305}.
SEQUENCE 891 AA; 97677 MW; EB47E5B3C3F9C56C CRC64;
MSSTLREASK DTLQAKDKTY HYYSLPLAAK SLGDITRLPK SLKVLLENLL RWQDGNSVTE
EDIHALAGWL KNAHADREIA YRPARVLMQD FTGVPAVVDL AAMREAVKRL GGDTAKVNPL
SPVDLVIDHS VTVDRFGDDE AFEENVRLEM ERNHERYVFL KWGKQAFSRF SVVPPGTGIC
HQVNLEYLGK AVWSELQDGE WIAYPDTLVG TDSHTTMING LGVLGWGVGG IEAEAAMLGQ
PVSMLIPDVV GFKLTGKLRE GITATDLVLT VTQMLRKHGV VGKFVEFYGD GLDSLPLADR
ATIANMSPEY GATCGFFPID AVTLDYMRLS GRSEDQVELV EKYAKAQGMW RNPGDEPIFT
STLELDMNDV EASLAGPKRP QDRVALPDVP KAFAASNELE VNATHKDRQP VDYVMNGHQY
QLPDGAVVIA AITSCTNTSN PSVLMAAGLL AKKAVTLGLK RQPWVKASLA PGSKVVSDYL
AKAKLTPYLD ELGFNLVGYG CTTCIGNSGP LPDPIETAIK KSDLTVGAVL SGNRNFEGRI
HPLVKTNWLA SPPLVVAYAL AGNMNINLAS EPIGHDRKGD PVYLKDIWPS AQEIARAVEQ
VSTEMFRKEY AEVFEGTAEW KGINVTRSDT YGWQEDSTYI RLSPFFDEMQ ATPAPVEDIH
GARILAMLGD SVTTDHISPA GSIKPDSPAG RYLQGRGVER KDFNSYGSRR GNHEVMMRGT
FANIRIRNEM VPGVEGGMTR HLPDSDVVSI YDAAMRYKQE QTPLAVIAGK EYGSGSSRDW
AAKGPRLLGI RVVIAESFER IHRSNLIGMG ILPLEFPQGV TRKTLGLTGE EKIDIGDLQN
LQPGATVPVT LTRADGSQEV VPCRCRIDTA TELTYYQNDG ILHYVIRNML K


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