>TIGR00117 acnB aconitate hydratase 2; InterPro: IPR004406 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated . IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents bacterial aconitase B (AcnB) enzymes, which can switch between aconitase enzyme activity and post-translational gene regulation. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0003994 aconitate hydratase activity, 0005515 protein binding, 0051539 4 iron 4 sulfur cluster binding, 0006099 tricarboxylic acid cycle.

Probab=99.83 E-value=7.6e-19 Score=156.75 Aligned_cols=453 Identities=24% Similarity=0.331 Sum_probs=281.6 Q ss_pred HHHCCCHHHHHHHHHHHHCC-------------------CCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHEECCCCH Q ss_conf 54457119999998874048-------------------66579999999861235545777663645325220000035 Q gi|254780451|r 37 ISRLPCSMKVLLENLLRFED-------------------GCTVTKEQIHAFVKWLDNKGTVESEVSYRFSRVLMQDFTGV 97 (896) Q Consensus 37 ~~~lP~s~rillEn~~R~~~-------------------~~~~~~~~~~~~~~w~~~~~~~~~ei~f~p~Rv~~qD~Tg~ 97 (896) T Consensus 344 ~g~~p~~~g~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~~~~~g~~cg~--~g~~pg~~c~p~~~~~g~~d~~g~ 421 (864) T TIGR00117 344 GGRIPLLIGRGLTDKAREALGLGPSPLFKKPSAPADDGKGFTLAQKLVGKACGV--KGIRPGTYCEPKLTTVGSQDTTGP 421 (864) T ss_pred CCCCEEEECCCCHHHHHHHHCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHCCC--CCCCCCCCCCCCEEECCCCCCCCC T ss_conf 674113430310023466516872100004444322344303566665323032--224676433531000366444443 Q ss_pred HHHHHHHHHHHHHHHCCCCHHHCCCCCCEEEEEECCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEC Q ss_conf 79999999999999719999992878981399868321100599889998999887542678999987742148807860 Q gi|254780451|r 98 PAVVDLAAMRDAIVVLGGDPQNINPLVPVDLVIDHSLIVDYSGNKDAVTRNKDLEYQRNEERYRFLKWGQKSFKNFRVVP 177 (896) Q Consensus 98 pa~vdlaamR~~~~~~g~dp~~inp~vp~dlviDHsv~vd~~g~~~a~~~n~~~e~~rN~Ery~Flkwa~~~f~~~~v~p 177 (896) T Consensus 422 ~~~d~~~~----~~~~~~~~~~~---------~------~~~c~~~~~p~p~d~~~--~~~~p~~~~--~---~gg~~~~ 475 (864) T TIGR00117 422 LTRDELKE----LACLGFDADLV---------L------QSFCHTAAYPKPVDVST--HATLPDFIT--N---RGGVALR 475 (864) T ss_pred CCHHHHHH----HHHHCCCCCHH---------H------HHHHHHHCCCCCCCCCC--CCCCCHHHH--C---CCCEEEC T ss_conf 20566666----66512563134---------5------54443303676443310--001212343--1---5760224 Q ss_pred CCCCCHHHHHHHHHCCCEEEECCCCCEEEEEEEE-EECCCCCCCCCCCHHHHCCCCHHHHHHHHCCCCCEECCCCEEEEE Q ss_conf 8876216778986335113103688617983013-206887644452012320343489999970775141167289999 Q gi|254780451|r 178 PGTGICHQINLEYLGQSVWTKNENGENIAYPDTC-VGTDSHTTMINALGILGWGVGGIEAEAAMLGCPISMLLPEVVGFE 256 (896) Q Consensus 178 PG~GI~HQvnlE~la~vv~~~~~~~~~~a~Pdtl-VGtDSHT~~~galG~la~GVGg~eaea~mlGqp~~~~vPevigv~ 256 (896) T Consensus 476 pgdg~~~~w~~---------------~~~~pd~~g~ggd~~~~~p~g~~-~p~g~g-~~~~~~~~g~-~p~~~p~~~~~~ 537 (864) T TIGR00117 476 PGDGVIHSWLN---------------RLLLPDTLGTGGDSHTRFPLGIS-FPAGSG-LVAFAAATGV-LPLDLPESVLVR 537 (864) T ss_pred CCCCHHHHHHH---------------HHCCCCCCCCCCCCCCCCCCEEC-CCCCCC-HHHHHHHHCC-CCCCCCCCEEEE T ss_conf 66413677665---------------41265223578754321211001-456552-3334454313-325664000011 Q ss_pred EECCCCCCCCHHHHHHHHHHHHCCCCC------------CCEEEEEEECCCCCCCHHHHHHHHCCCCCCCCCEEEECCCH Q ss_conf 976778644368899999998410221------------21279996155001787563212000100372037751998 Q gi|254780451|r 257 VTGSLQEGVTATDLVLTITQMLRKEGV------------VSKFVEFFGSGFESMVLADRATIANMAPEYGATCGFFPVDR 324 (896) Q Consensus 257 L~G~L~~gVtakDiiL~i~~~Lr~~Gv------------vgk~vEf~G~gi~~LS~~dRaTIaNMa~E~GAt~gifp~De 324 (896) T Consensus 538 ~~g~~~pg~~~~d~~~~~p~~~~~~g~~~~~~~~~~~~~~g~~~~~~--g~pd~~~~~~~~~~d~~~~~~~~~~~~~~~~ 615 (864) T TIGR00117 538 FKGELQPGITLRDLVNAIPWYAIKQGLLTVEKKGKVNVFNGRILEIE--GLPDLKVEQAFELTDASAERSAAGCTIKLNK 615 (864) T ss_pred ECCCCCCCCHHHHHHHHHHHHHHHCCCEEECCCCCEEECCCCEEEEC--CCCCCHHHHHHHHCCCHHHHHHCCCEEECCH T ss_conf 21334667227777654223444202201025662010145123314--7774102222211000011100110232130 Q ss_pred H-HHHHHHHC----------CCCHH-----HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCC-CCHHCCCCCCCC Q ss_conf 9-99999863----------99988-----9999998746410236767667886306999980314-301226566564 Q gi|254780451|r 325 G-TIDYLRLS----------GRSNS-----RVDLVEAYTKVQGMWREDIDYEKVAFTKKMKLDLGNV-SPSVAGPRRPES 387 (896) Q Consensus 325 ~-T~~YL~~t----------GR~~~-----~v~lve~Y~ka~~l~~~~~~d~~a~Y~~vieiDLs~i-eP~VAgP~~P~d 387 (896) T Consensus 616 ~~~~~~~~~~~~~~~~~~~~g~~d~~~~~~~~~~~~~w~~~p~~~---~~d~~~~~~~~~~~~~~~~~~p~~~~p~dpd~ 692 (864) T TIGR00117 616 EPVIEYLKSNIVLLKWLIAEGYGDKRTLLRRIDGLEEWLANPELL---EGDADAEYAAVIEIDLAEIKEPILAAPNDPDD 692 (864) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCC---CCCCCCCHHHHHHCCHHHHCCCCEECCCCCHH T ss_conf 257887630156666776404312688999988888752361010---56554201332110244511220106897212 Q ss_pred EEEHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 13677730116687664001100232102457888887555445753104676545999877889998898649875867 Q gi|254780451|r 388 RLSLSEVPSSFVTEMNEYYKKSHTLDEKYPVKGCDFHLKHGDVAIASITSCTNTFNPSVMIGAGLLARNAVRAGLKSKPW 467 (896) Q Consensus 388 ~v~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~VvIAaIgSCTNtSnp~~miaAgllAkkAv~~Glkv~p~ 467 (896) T Consensus 693 ~~~~~~~~~~~------~g~~p~~~~~------------------~~~g~c~~--~~g~~~~~~~~~~-----~~~g~~~ 741 (864) T TIGR00117 693 VKPLSEVLGDT------TGKRPHAIDE------------------VFIGSCLT--NIGHFRAAGKLLD-----GAPGPLP 741 (864) T ss_pred HHHHHHHHHHC------CCCCCCHHHH------------------HHHHHHHH--HHHHHHHHHHHHH-----CCCCCCC T ss_conf 56777764101------3666420223------------------33323443--2234556677763-----2687545 Q ss_pred CEEEEECCCHHHHHHHHHCCCHHHHHHHCCEECCCCCCCCCCCCCCCCCHHHHHCCCCCEEEEEEECCCCCCCCCCCCCC Q ss_conf 30797016189999999858857777505302055322421277768830221011366358786336766665468543 Q gi|254780451|r 468 VKTSCAPGSQVSYEYLVQAGLVEYLEALGFSLVGFGCTTCIGNSGALKKEISEVIHQKSLVVAGVLSGNRNFEGRISPDV 547 (896) Q Consensus 468 Vkt~l~PGS~~V~~~L~~~Gll~~L~~aGf~i~~~GCg~CiGnsG~l~~~i~~~i~~~~l~~~sV~SgNRNFeGR~~p~~ 547 (896) T Consensus 742 ~~~w~~pp~~~d~~~~~~~g~~~~~~~~g~~~~~pgc~~c~g~~~~~--------~d~~-~--~~~~~~~~~~~~~g~g~ 810 (864) T TIGR00117 742 GRLWVAPPTRLDEQELTEEGYYGIFGAAGARTEVPGCSLCLGNQARV--------EDGA-T--VFSTSTRNFPNRLGKGA 810 (864) T ss_pred CEEEECCCCCCCHHHHHHCCCHHHHHCCCCCCCCCCCCEECCCCCHH--------CCCC-E--EEEECCCCCCCCCCCCC T ss_conf 31574175422057765322021010245421167410002651000--------0561-4--76402344430026652 Q ss_pred CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC Q ss_conf 310005978999998516122231002355488886320015688857888887641583 Q gi|254780451|r 548 EANYLLSPPLVVAYALAGNVRKNLIKDPIGEDQQGSPVYLRDIWPKDSEIQSFVNKYVTC 607 (896) Q Consensus 548 ~~~yLaSP~lVvA~AiaG~I~~d~~~dplg~~~~G~~v~L~DiwPs~~Ei~~~~~~~v~~ 607 (896) T Consensus 811 ~~-~~~~~~~~~~~~~~g~~------------------------p~~~~~~~~~~~~~~~ 845 (864) T TIGR00117 811 KV-YLGSAELAAVCALLGKL------------------------PTPEEYLTLVSEKLEP 845 (864) T ss_pred EE-EECHHHHHHHHHHHHCC------------------------CCHHHHHHHHHHHHHH T ss_conf 02-21114677899876046------------------------7667888888766433

HHsearch alignment for GI: 254780451 and conserved domain: TIGR00117