HHsearch alignment for GI: 254780451 and conserved domain: TIGR02084
>TIGR02084 leud 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011824 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry contains predominantly bacterial 3-isopropylmalate dehydratase enzymes. The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases 4.2.1 from EC and bind a [4Fe-4S]-cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=99.39 E-value=8.5e-14 Score=119.88 Aligned_cols=153 Identities=28% Similarity=0.368 Sum_probs=100.1
Q ss_pred EEEECCCCCHHHCCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHCCCCCCCCCCEEEC
Q ss_conf 99965885723316456555447378889874988656314565302357776652036012232125777657722453
Q gi|254780451|r 669 LCLLGDKITTDHISPAGSIPLQSAAASYLRQRGVKEKDFNQFGTRRGNHEVMMRGTFSNIRICNYMLGEEGKKGGYTIHY 748 (896)
Q Consensus 669 L~~lGD~iTTDHISPAG~I~~~spAg~yL~~~Gv~~~dfNsygsRRgNhevM~RGtFaNirl~N~l~~~~~~egg~T~~~ 748 (896)
T Consensus 3 ~~~~Gdn~~td~iiPa----------rylnt~--~~~ela~~--------~me-----------------d~~~~f~--- 42 (156)
T TIGR02084 3 VLKYGDNVDTDVIIPA----------RYLNTS--DPKELAKH--------CME-----------------DLDKEFK--- 42 (156)
T ss_pred EEEECCCCCCCCCCCH----------HHHCCC--CHHHHHHH--------HHH-----------------HHHHHHH---
T ss_conf 2540575464511221----------331135--76789999--------886-----------------3356776---
Q ss_pred CCCCEEEHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHCCEEEEEECCHHHHHHHCCCCCEEEEEECCCCCCH
Q ss_conf 89978737999998998199889994677786730799988667617089997647898885053552322331789898
Q gi|254780451|r 749 PSKEELFIYDAAMRYKVDQVPLVVFAGVEYGNGSSRDWAAKGTRLLGVRSVIAESFERIHRSNLIGMGVIPFAFGKGISW 828 (896)
Q Consensus 749 p~~~~~~iydaA~~Y~~~~~plVViAG~~YG~GSSRdwAAkgp~lLGVkAVIA~SFeRIHrsNLv~mGiLPL~F~~~~~~ 828 (896)
T Consensus 43 ---------------~~~~~G~i~v~G~nfG~GssrehaP~~ik~~G~~~~iaksfarif~rn~iniGl~i~e~~e--~~ 105 (156)
T TIGR02084 43 ---------------KKVKEGDIIVAGENFGCGSSREHAPIAIKASGISCVIAKSFARIFYRNAINIGLPIVESEE--AV 105 (156)
T ss_pred ---------------HHHCCCCEEEECCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHH--HH
T ss_conf ---------------5421575687214336777644342221003720002446777876534541213200467--88
Q ss_pred HHHCCCCCEEEEEECHHHCCCCCEEEEEEEECCCCEEEEEEEEEECCHHHHHHHHCCCHHHHHH
Q ss_conf 8819897438997263225899738999981899679999998738999999999098368988
Q gi|254780451|r 829 KNLNIKGDEIINIRKLKTISPRQESTLEIHYSDGTFKCVPIICCIDTLDEINHLKNGGILQAVL 892 (896)
Q Consensus 829 ~~L~l~G~E~~~i~~~~~l~p~~~v~v~i~~~~g~~~~~~~~~r~dt~~E~~~~~~GGiL~yvl 892 (896)
T Consensus 106 ~~~~-~Gd-~~~vd~~~G~~~------n~~--~~--~~~~~--~~fP~~~~~i~~~~G~~~~~~ 155 (156)
T TIGR02084 106 DEIE-EGD-EVEVDLEKGIIK------NVT--KG--KEYKA--QPFPEFLQEILKAGGLLNYVK 155 (156)
T ss_pred HHHH-CCC-EEEEEHHHHHHH------HHH--CC--CCCCC--CCCHHHHHHHHHCCCHHHHHC
T ss_conf 6530-587-588733022666------520--46--42112--112189999985154444651