>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.

Probab=99.98 E-value=1.3e-32 Score=257.53 Aligned_cols=391 Identities=20% Similarity=0.253 Sum_probs=254.2 Q ss_pred CCCCCCCCCCCCCCCHHHHHHH-----------C-CCCCCCC-EEEEECCCCCCHHHHHHHHHHHHHCC----------- Q ss_conf 3334556663237812488886-----------5-9857870-89995498751889999999998503----------- Q gi|254780334|r 62 SEESIEEESRIQTHIDELDRVT-----------G-GGFVRGS-VILVGGDPGIGKSTLLMQTAASLAYK----------- 117 (479) Q Consensus 62 ~~~~~~~~~Ri~TGi~eLDrvL-----------G-GGl~~Gs-~~Li~G~PGvGKSTL~Lqia~~~a~~----------- 117 (479) T Consensus 409 LD~DHYGL~~VK~RIlEYlAV~qllemrrkkkPkL~~~~~GpqIlClvGPPGVGKTSlg~SIA~ALnRkFvR~SlGG~~D 488 (941) T TIGR00763 409 LDEDHYGLKKVKERILEYLAVQQLLEMRRKKKPKLRGKMKGPQILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRD 488 (941) T ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCEEEEEEECCCEE T ss_conf 31678888773034135888989998764036444778888767872072695422278999999688049995267220 Q ss_pred -----CCCEEEEECCCCHHHHHHHHHHCCCCCCCHHEECCCCHHHHH-HHHHHCCCCC---EEEECHHHH-HHHHHHCCC Q ss_conf -----981999986463047888875201577510000347889999-9997316982---899721687-665420445 Q gi|254780334|r 118 -----KHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDII-ATLITNEKPD---LVIIDSIQT-LWSQTAESS 187 (479) Q Consensus 118 -----g~~vlYvS~EEs~~Qi~~Ra~Rl~~~~~~i~~~~e~~l~~il-~~~i~~~~~~---~vVIDSIQt-l~~~~~~s~ 187 (479) T Consensus 489 eAEIrGHRRTYvGAM--PGriiQ~lk~~~t~-NPl~LlDEID--K~~~~~-~~~GDPaSALLEvLDPEQN~~F~DHYldv 562 (941) T TIGR00763 489 EAEIRGHRRTYVGAM--PGRIIQGLKKAKTK-NPLILLDEID--KIGLKS-SFRGDPASALLEVLDPEQNNAFSDHYLDV 562 (941) T ss_pred HHHCCCCCCCCCCCC--HHHHHHHHHHCCCC-CCEEEEEEEE--EECCCC-CCCCCHHHHHHHHCCHHHCCCCCCCCCCC T ss_conf 311278643203467--25789998760415-8806862022--001678-86556378886412864360425530023 Q ss_pred CCCHHHHH--HHH--------------------------HHHHHHHHHCCCEEEEEEEECCCCCCC-CHHHHHHHHHEEE Q ss_conf 56367999--999--------------------------999997530797899986303665433-1145787753027 Q gi|254780334|r 188 PGTVIQVR--TSV--------------------------QAMIQYAKKNGVAMVLVGHVTKEGQIA-GPRVIEHMVDAVL 238 (479) Q Consensus 188 ~GsvsQvr--e~~--------------------------~~L~~~AK~~~i~vilighvTK~G~iA-Gp~~LeH~VD~vl 238 (479) T Consensus 563 p~DLS~V~CyFi~TAN~~d~IP~PLLDRMEvI~lsGY~~~EK~~IA~~yLiP~~~~~~GL~~~~l~~~d~al~~lI~~Yt 642 (941) T TIGR00763 563 PFDLSKVLCYFIATANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKISDEALLLLIKYYT 642 (941) T ss_pred CCCHHHHHHHEEECCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCHHHHHHHHCCCCCCEEECHHHHHHHHHHHH T ss_conf 40042002100024475767772213740245238887678999998547136798708881322126899999998751 Q ss_pred EEECCCCCCCCCCEEEEE-----EEE----------------------------------C-----------CCCCCCEE Q ss_conf 851555666544215676-----320----------------------------------2-----------56765127 Q gi|254780334|r 239 YFEGGTRNTQYDYRILRS-----VKN----------------------------------R-----------FGPTDEIG 268 (479) Q Consensus 239 ~~ege~~~~~~~~R~Lr~-----~KN----------------------------------R-----------fG~t~e~g 268 (479) T Consensus 643 REaGVRNL~r~I~~i~RK~A~~~~~~~~~~~~P~~~~dp~ea~~~e~~~e~~~k~~~e~~~~~~~~~~~~~~~~~~~~~~ 722 (941) T TIGR00763 643 REAGVRNLERQIEKICRKAAVKLVEQVKEEEEPAEAADPKEAEGGEKKKERTKKKTSEKSSDQESEKEKSEIQLKKSEKE 722 (941) T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 32021338999999999999999871463337763477112046665567554656765643345774000100137631 Q ss_pred EEEECCCCCEEECCHHHHHHC-CCC-CCCCCEEEEEEECCCCCCEEEEEEEECCC-----CCCCCEEEEEC----CCHHH Q ss_conf 998515663110140455511-476-67673489973048974115533101157-----78772477604----68666 Q gi|254780334|r 269 VFEMSDKGLQEVSDPSKIFLS-DRD-STSPGTAVFAGIEGTRALLVEIQSLVVPT-----SLGMPRRTVVG----WDSSR 337 (479) Q Consensus 269 vf~m~~~Gl~~v~~ps~~fl~-~~~-~~~~Gs~v~~~~eG~r~~lvEvQALv~~~-----~~~~p~R~~~G----~d~~r 337 (479) T Consensus 723 ~~~i~~~~L~~ylG~p~F~~~E~~~~~~~pGvV~GLAWT~~GG~~L~iEt~~~~gq~Dl~~~kkG~L~lTGqLGDVMKES 802 (941) T TIGR00763 723 SVEITEDNLKKYLGKPVFTSEERAYETTPPGVVMGLAWTPMGGDTLFIETTKVAGQKDLKGDKKGSLELTGQLGDVMKES 802 (941) T ss_pred EEEECHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCEECCCCCEEEEEEEEEECCCCCCCCCCCCCEEECCCCCHHHHHH T ss_conf 37854678886528963064545545789856873322324771310447976374034668898667715652599999 Q ss_pred HHHHHHHHHHHC------C----CCCCCCHHHEECCCC-CCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEEECCCEE Q ss_conf 555589887511------1----102462221001456-11154325879999999972488688785999874247316 Q gi|254780334|r 338 LAMILAVLEARC------N----IKFGNHDVHLNIAGG-YRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSV 406 (479) Q Consensus 338 l~~llAvl~k~~------~----~~~~~~Di~~nv~gG-~~i~~pa~DLaia~ailSs~~~~~~~~~~~~~GEl~L~GeI 406 (479) T Consensus 803 A~~Alt~~r~~~~~~~i~~~~~l~ff~~~diH~HvPEGAtPKDGPSAG~tm~TaL~Sl~~~~~Vr~~~AMTGE~TLrG~V 882 (941) T TIGR00763 803 AQIALTYVRSIAEDLGISPPKVLKFFEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRADVAMTGEITLRGKV 882 (941) T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCE T ss_conf 99999999999986188870234253226520213788989886247999999999997087988553551004102356 Q ss_pred EEECCHHHHHHHHHHCCCCEEEECHHHH-HHCC------CCCEEEEEECCHHHHHHHHH Q ss_conf 3407889999999976998999775765-3228------58808998383999999861 Q gi|254780334|r 407 RAVGHMQQRLKEAEKIGFLSGVFPESAK-GECK------IGMLDRQYIKNLSDLVKKIT 458 (479) Q Consensus 407 R~V~~i~~ri~eA~~~G~~~~iiP~~n~-~e~~------~~~i~i~~v~~l~e~i~~l~ 458 (479) T Consensus 883 LpiGGlKEK~iAA~R~Gik~iilP~~N~e~Dl~elP~~v~e~L~~~~V~~~~ev~~~af 941 (941) T TIGR00763 883 LPIGGLKEKTIAAKRAGIKTIILPEKNRERDLEELPENVKEGLEIHFVKHYDEVLKKAF 941 (941) T ss_pred EEECCHHHHHHHHHHHCEEEEECCCHHHCCCHHHHHHHHHHCCCEEEHHHHHHHHHHHC T ss_conf 20050468888853505007774612001526620398872784110032789999829

HHsearch alignment for GI: 254780334 and conserved domain: TIGR00763